Re: [gmx-users] H-atoms in .hdb file

[Shima Arasteh]

I added the FOR residue as protein in residuetypes.dat file, but still says 
it's not identified as protein/DNA/RNA. 

Would you mind helping me with your suggestions?

Thanks in advance

 
Sincerely,
Shima


- Original Message -
From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Tuesday, June 26, 2012 8:20 PM
Subject: Re: [gmx-users] H-atoms in .hdb file



On 6/26/12 11:47 AM, Shima Arasteh wrote:
> OK, but when I chose none, it gives me a fatal error ( dangling bond! ). A 
> new problem! So how do I solve it?
> 

"Dangling bond" errors were introduced as part of the output in Gromacs 4.5. 
The "aminoacids.dat" file was only used by older (4.0.x and earlier) versions 
of Gromacs.  You need to be modifying "residuetypes.dat" to indicate that FOR 
is a Protein residue so that the chain is continuous with respect to its 
content type.

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] H-atoms in .hdb file

[Shima Arasteh]

As Justin suggested me, I added the FOR residue to the .rtp file of FF and then 
added the FOR as a protein in residuetypes.dat . FOR is the first residue in 
protein chain. I chose none as the N-terminus . But after processing the .pdb 
file the FOR is identified itself but "not" identified as protein. 

Any suggestion please?

Thanks in advance
Sincerely,
Shima



From: Mark Abraham 
To: Shima Arasteh  
Sent: Wednesday, June 27, 2012 11:54 AM
Subject: Re: [gmx-users] H-atoms in .hdb file


On 27/06/12, Shima Arasteh   wrote:
I added the FOR residue as protein in residuetypes.dat file, but still says 
it's not identified as protein/DNA/RNA. 
>
>Would you mind helping me with your suggestions?

Apparently it's not been done right, but we don't have enough detail about what 
you've done to know what you've done wrong. Look carefully at the contents of 
the file you changed, and inspect your output carefully for clues.

Mark

>
>Thanks in advance
>
> 
>Sincerely,
>Shima
>
>
>- Original Message -
>From: Justin A. Lemkul 
>To: Discussion list for GROMACS users 
>Cc: 
>Sent: Tuesday, June 26, 2012 8:20 PM
>Subject: Re: [gmx-users] H-atoms in .hdb file
>
>
>
>On 6/26/12 11:47 AM, Shima Arasteh wrote:
>> OK, but when I chose none, it gives me a fatal error ( dangling bond! ). A 
>> new problem! So how do I solve it?
>> 
>
>"Dangling bond" errors were introduced as part of the output in Gromacs 4.5. 
>The "aminoacids.dat" file was only used by older (4.0.x and earlier) versions 
>of Gromacs.  You need to be modifying "residuetypes.dat" to indicate that FOR 
>is a Protein residue so that the chain is continuous with respect to its 
>content type.
>
>http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>
>-Justin
>
>-- 
>
>Justin A. Lemkul, Ph.D.
>Research Scientist
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
>
>
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Re: [gmx-users] wrong distances with g_dist

[lloyd riggs]

Dear Dmytro Kovalskyy,

The ARG CZ is at the end (tip of the ARG), what does the distances look like 
over time?  A floppy long amino acid?  And your actual distance calculation?  
Is it from a graphics/pdb file, or how is it measured?

Stephan

 Original-Nachricht 
> Datum: Tue, 26 Jun 2012 16:14:31 -0500
> Von: Dmytro Kovalskyy 
> An: gmx-users@gromacs.org
> Betreff: [gmx-users] wrong distances with g_dist

> Hi,
> 
> I try to calculate distance between two atoms with g_dist. Somewhat I get 
> distance lower than actual.
> Here there are coordinates of the two atoms (PDB format)
>  
> ATOM702  CZ  ARG X  45   5.930   9.230  41.740  0.00  0.00
> ATOM   2751  CA  PHE X 177  41.710  45.000  27.180  0.00  0.00
> 
> And the distance I get from g_dist is 4.6260725 nm while the actual is
> 5.265 
> nm.
> 
> What the problem can be?
> 
> Dmytro
> 
> 
> 
> 
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[gmx-users] error using grompp: number of coordinates in coordinate file does not match topology

[reisingere]

Hi everybody,
I am going through the tutorial for membrane protein simulation which is
offered by gromacs.
I did everything just like it is described in the tutorial but when I want
to do the minimization in Step 3 after packing the lipids around the
protein I always get the error the
"number of coordinates in coordinate file (system_inflated.gro, 9900)
 does not match topology (topol.top, 3800)"
I understand why it is like that because I just append the membrane to the
protein file but how can I also change the topology file?


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html


Bests, Eva

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Re: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

[Justin A. Lemkul]

On 6/27/12 1:23 AM, rama david wrote:

Hi Gromacs Friends,
 I am doing Justin-lipid tutorialer
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html

In these the npt.mdp has a parameter
refcoord_scaling = com
Why these parameter is introduced in NPT of lipid-protein simulation
  and not use in Lysozyme in water simulation ???



It is used in the lysozyme tutorial.  Some time ago, I was informed that the 
line was missing from the .mdp file, so if you completed the tutorial during 
that time, the line was missing.  grompp should have produced an obvious 
warning, however.



Please give the detail on why to use these parameter??



If the reference coordinates are not scaled, you can get spurious contributions 
to the virial and pressure.  There is some discussion on this (admittedly not 
much) in the manual.


-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] H-atoms in .hdb file

[Justin A. Lemkul]

On 6/27/12 3:38 AM, Shima Arasteh wrote:



As Justin suggested me, I added the FOR residue to the .rtp file of FF and then added the 
FOR as a protein in residuetypes.dat . FOR is the first residue in protein chain. I chose 
none as the N-terminus . But after processing the .pdb file the FOR is identified itself 
but "not" identified as protein.



How so?  What line did you add to residuetypes.dat, and what was the exact 
problematic output of pdb2gmx?


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] error using grompp: number of coordinates in coordinate file does not match topology

[Justin A. Lemkul]

On 6/27/12 4:31 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Hi everybody,
I am going through the tutorial for membrane protein simulation which is
offered by gromacs.
I did everything just like it is described in the tutorial but when I want
to do the minimization in Step 3 after packing the lipids around the
protein I always get the error the
"number of coordinates in coordinate file (system_inflated.gro, 9900)
  does not match topology (topol.top, 3800)"
I understand why it is like that because I just append the membrane to the
protein file but how can I also change the topology file?



With a text editor.  The content of the [molecules] directive must always agree 
with the contents of the coordinate file, with respect to number of molecules 
and the order in which the molecules appear.  You likely need to add a line in 
this directive indicating the number of DPPC molecules, which appears to be 122 
(9900-3800 = 6100 = 122 * 50).


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] H-atoms in .hdb file

[Shima Arasteh]

I added this line to the residuetypes.dat file:
FOR   Protein

Then running this command:
pdb2gmx -f protein.pdb -water spc -ter

Written as blow:

Processing chain 1 (177 atoms, 25 residues)
Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA.
Identified residue VAL1 as a starting terminus.
Identified residue GLY24 as a ending terminus.

Asked for terminus:
I chose "none" as the N-terminus.
 
Getting this:
 Processing chain 1 (177 atoms, 25 residues)
Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA.
Identified residue VAL1 as a starting terminus.
Identified residue GLY24 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for VAL-1
 0: NH3+
 1: NH2
 2: None
2
Start terminus VAL-1: None
Select end terminus type for GLY-24
 0: COO-
 1: COOH
 2: None
0
End terminus GLY-24: COO-

---
Program pdb2gmx, VERSION 4.5.5
Source code file: 
/home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c, line: 1035

Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a proper 
terminal entry.


Would you helping me with it with your useful suggestions?




Sincerely,
Shima


- Original Message -
From: Justin A. Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc: 
Sent: Wednesday, June 27, 2012 2:58 PM
Subject: Re: [gmx-users] H-atoms in .hdb file



On 6/27/12 3:38 AM, Shima Arasteh wrote:
>
>
> As Justin suggested me, I added the FOR residue to the .rtp file of FF and 
> then added the FOR as a protein in residuetypes.dat . FOR is the first 
> residue in protein chain. I chose none as the N-terminus . But after 
> processing the .pdb file the FOR is identified itself but "not" identified as 
> protein.
>

How so?  What line did you add to residuetypes.dat, and what was the exact 
problematic output of pdb2gmx?

-Justin

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Fwd: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

[rama david]

 Thank you Justin for your Explaination

 Please Would you me the Reason Why these parameter is present in
 Equilibration mdp and
 not in production run mdp file ( for both lysozyme and lipid simulation )

 With Best Wishes and regardsRama
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Re: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

[Justin A. Lemkul]

On 6/27/12 7:01 AM, rama david wrote:


Thank you Justin for your Explaination

Please Would you me the Reason Why these parameter is present in Equilibration
mdp and
not in production run mdp file ( for both lysozyme and lipid simulation )




It is only relevant when applying position restraints.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

[rama david]

Thank you Justin,

But you not added these parameter to the
Umbrella sampling NPT file.
Is any reason not to use these parameter  in Umbrella sampling??

I run the simulation of peptide withought any
refcoord_scaling = com in mdp  file
and now  is it will affect result  significantly??
Is it wrong simulation???

How to check these parameter affect my result sensitivity???

Please give me valuable guidance to solve my query..

With Best Wishes and regards,
Rama David
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Re: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

[Justin A. Lemkul]

On 6/27/12 7:16 AM, rama david wrote:

Thank you Justin,

But you not added these parameter to the
Umbrella sampling NPT file.
Is any reason not to use these parameter  in Umbrella sampling??



If it is missing, it's a simple typographical omission.  I have adapted these 
tutorials over many years and occasionally something like this slips through the 
cracks.  Hence why it's always important to pay attention to the warnings grompp 
prints out.



I run the simulation of peptide withought any
refcoord_scaling = com in mdp  file
and now  is it will affect result  significantly??
Is it wrong simulation???

How to check these parameter affect my result sensitivity???



The pressure might be slightly off.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] H-atoms in .hdb file

[Justin A. Lemkul]

On 6/27/12 6:38 AM, Shima Arasteh wrote:



I added this line to the residuetypes.dat file:
FOR   Protein

Then running this command:
pdb2gmx -f protein.pdb -water spc -ter

Written as blow:

Processing chain 1 (177 atoms, 25 residues)
Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA.
Identified residue VAL1 as a starting terminus.
Identified residue GLY24 as a ending terminus.

Asked for terminus:
I chose "none" as the N-terminus.

Getting this:
  Processing chain 1 (177 atoms, 25 residues)
Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA.
Identified residue VAL1 as a starting terminus.
Identified residue GLY24 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for VAL-1
  0: NH3+
  1: NH2
  2: None
2
Start terminus VAL-1: None
Select end terminus type for GLY-24
  0: COO-
  1: COOH
  2: None
0
End terminus GLY-24: COO-

---
Program pdb2gmx, VERSION 4.5.5
Source code file: 
/home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c, line: 1035

Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a proper 
terminal entry.


Would you helping me with it with your useful suggestions?



I honestly have no idea why that's not working.  It's the exact same workflow 
used with all other capping groups and I use it routinely.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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[gmx-users] About Exclusion of bonded and non bonded parameters while running grompp

[PAVAN PAYGHAN]

Dear Gromacs Users,

I am using gromacs version 4.5.5. , while running grompp (for any
purpose i.e. minimization , equilibration etc. )
I am getting following screen output without any warning, error or
note relevant to it.
"Generated 830 of the 2346 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 3 bonded neighbours molecule type 'Protein_B'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL' "
My question is whether to ignore or consider this as an error ?
I really don't know why this screen output is coming which I never
faced ? Is there any mistake by me ?  Please suggest .

cg.mdp for reference
; Conjugate Minimization
; Protein - Water - Ligand ( all free to move)
;
;
;
Title = Pro-Lig H2O
define = -DFLEXIBLE ; specifies flexible water
constraints = none
integrator = cg
nsteps = 2000
ns_type = grid
rlist = 1.2
coulombtype = pme
vdw-type = cut-off
rvdw = 1.2
rcoulomb = 1.2
;
; Energy Minimization Stuff
;
;
emtol = 0.001
emstep = 0.01


Thanking you in advance .

Regards,

Pavan Payghan
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Re: [gmx-users] About Exclusion of bonded and non bonded parameters while running grompp

[Justin A. Lemkul]

On 6/27/12 7:36 AM, PAVAN PAYGHAN wrote:

Dear Gromacs Users,

I am using gromacs version 4.5.5. , while running grompp (for any
purpose i.e. minimization , equilibration etc. )
I am getting following screen output without any warning, error or
note relevant to it.
"Generated 830 of the 2346 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_A'
Excluding 3 bonded neighbours molecule type 'Protein_B'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL' "
My question is whether to ignore or consider this as an error ?


This output is perfectly normal, and is (or at least, should be) present for any 
system that has more than monoatomic species.



I really don't know why this screen output is coming which I never
faced ? Is there any mistake by me ?  Please suggest .



There is no mistake.  Please refer to the manual, section 4.6.1.

-Justin


cg.mdp for reference
; Conjugate Minimization
; Protein - Water - Ligand ( all free to move)
;
;
;
Title = Pro-Lig H2O
define = -DFLEXIBLE ; specifies flexible water
constraints = none
integrator = cg
nsteps = 2000
ns_type = grid
rlist = 1.2
coulombtype = pme
vdw-type = cut-off
rvdw = 1.2
rcoulomb = 1.2
;
; Energy Minimization Stuff
;
;
emtol = 0.001
emstep = 0.01


Thanking you in advance .

Regards,

Pavan Payghan



--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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[gmx-users] Pulling ligand - Different Profiles (Force vs time)

[Steven Neumann]

Dear Gmx Users,

I obtained a protein-ligand complex from 100ns simulation. Now I am
pulling my ligand away from the protein after the energy minimzation
in water and equilibration of 100ps (two coupling baths: Protein,
LIG_Water_and_ions).
Then I proceed my pulling :

grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr

mdrun -s pull.tpr -deffnm pull


title   = Umbrella pulling simulation
define  = -DPOSRES
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 50    ; 1 ns
nstcomm = 10
; Output parameters
nstxout = 0
nstvout = 0
nstfout = 500
nstxtcout   = 1000   ; every 1 ps
nstenergy   = 500
; Bond parameters
constraint_algorithm    = lincs
constraints = all-bonds
continuation    = yes   ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb    = 1.4
rvdw    = 1.2
vdwtype = Switch
rvdw-switch = 1.0
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft    = yes
; Temperature coupling is on
tcoupl  = V-rescale      ; modified
Berendsen thermostat
tc_grps = Protein LIG_Water_and_ions   ; two coupling groups - more accurate
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 298   298      ; reference
temperature, one for each group, in K
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 2.0
compressibility = 4.5e-5
ref_p   = 1.0
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr    = EnerPres
; Pull code
pull    = umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim    = N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0 = Protein
pull_group1 = LIG
pull_rate1  = 0.004  ; 0.004 nm per ps = 4 nm per ns
pull_k1 = 500  ; kJ mol^-1 nm^-2

I run 3 pulling simulations with the same mdp  and I obtain 3
different profiles (Force vs time). Then I used 2xlonger pulling with
the same pulling distance and I run 3 simulations again. Each time I
obtain different profile. Can anyone explain me this? I am using
velocities from npt simulation as above (gen_vel = no and continuation
= yes) so I presume the output should be similar. Please, advice.

Steven
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Re: [gmx-users] Atoms get frozen with "Nose Hoover thermostat with Parrinello-Rahman barostat" for a system of an ion of charge +2 in flexible water molecules

[ms]

On 27/06/12 05:20, Surya Prakash Tiwari wrote:

Dear Gromacs users,

I am having a very strange problem with "Nose Hoover thermostat with
Parrinello-Rahman barostat" NPT simulations for a system of an ion of
charge +2 in flexible water molecules. Flexible water is taken from J.
Chem. Phys. 124, 024503 (2006); http://dx.doi.org/10.1063/1.2136877.
The ion is [UO2]2+ with charge on U=2.5 and each O has -0.25.

Atoms very soon get frozen after the simulation starts and they remain
frozen, they do not move at all. Only simulation box oscillates, which
causes atoms to oscillate little bit but they do not move at all.


To me it looks like a case of this artefact:

http://en.wikipedia.org/wiki/Flying_ice_cube

but I don't know exactly what is causing it in your system. Perhaps the 
article can help you triage...


--
Massimo Sandal, Ph.D.
http://devicerandom.org
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Re: [gmx-users] error using grompp: number of coordinates in coordinate file does not match topology

[reisingere]

Hi Justin,
thank you for your answer. Now it worked and I could do the minimization.
But now I have the same problem again but now the difference is 630.
So what I did is that I ran the minimization and everything worked. And
than I used the
"perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5
area_shrink1.dat"
command of the tutorial and now I got the error:
"number of coordinates in coordinate file (system_shrink1.gro, 9220)
 does not match topology (topol.top, 9850)"
But I changed nothing at the topology file.

Bests,
Eva
>
>
> On 6/27/12 4:31 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi everybody,
>> I am going through the tutorial for membrane protein simulation which is
>> offered by gromacs.
>> I did everything just like it is described in the tutorial but when I
>> want
>> to do the minimization in Step 3 after packing the lipids around the
>> protein I always get the error the
>> "number of coordinates in coordinate file (system_inflated.gro, 9900)
>>   does not match topology (topol.top, 3800)"
>> I understand why it is like that because I just append the membrane to
>> the
>> protein file but how can I also change the topology file?
>>
>
> With a text editor.  The content of the [molecules] directive must always
> agree
> with the contents of the coordinate file, with respect to number of
> molecules
> and the order in which the molecules appear.  You likely need to add a
> line in
> this directive indicating the number of DPPC molecules, which appears to
> be 122
> (9900-3800 = 6100 = 122 * 50).
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] error using grompp: number of coordinates in coordinate file does not match topology

[reisingere]

Got it already.
Thank you!!
>
>
> On 6/27/12 4:31 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi everybody,
>> I am going through the tutorial for membrane protein simulation which is
>> offered by gromacs.
>> I did everything just like it is described in the tutorial but when I
>> want
>> to do the minimization in Step 3 after packing the lipids around the
>> protein I always get the error the
>> "number of coordinates in coordinate file (system_inflated.gro, 9900)
>>   does not match topology (topol.top, 3800)"
>> I understand why it is like that because I just append the membrane to
>> the
>> protein file but how can I also change the topology file?
>>
>
> With a text editor.  The content of the [molecules] directive must always
> agree
> with the contents of the coordinate file, with respect to number of
> molecules
> and the order in which the molecules appear.  You likely need to add a
> line in
> this directive indicating the number of DPPC molecules, which appears to
> be 122
> (9900-3800 = 6100 = 122 * 50).
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
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> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>


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Re: [gmx-users] Pulling ligand - Different Profiles (Force vs time)

[Justin A. Lemkul]

On 6/27/12 7:48 AM, Steven Neumann wrote:

Dear Gmx Users,

I obtained a protein-ligand complex from 100ns simulation. Now I am
pulling my ligand away from the protein after the energy minimzation
in water and equilibration of 100ps (two coupling baths: Protein,
LIG_Water_and_ions).
Then I proceed my pulling :

grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr

mdrun -s pull.tpr -deffnm pull


title   = Umbrella pulling simulation
define  = -DPOSRES
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 50; 1 ns
nstcomm = 10
; Output parameters
nstxout = 0
nstvout = 0
nstfout = 500
nstxtcout   = 1000   ; every 1 ps
nstenergy   = 500
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes   ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.2
vdwtype = Switch
rvdw-switch = 1.0
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Temperature coupling is on
tcoupl  = V-rescale  ; modified
Berendsen thermostat
tc_grps = Protein LIG_Water_and_ions   ; two coupling groups - more accurate
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 298   298  ; reference
temperature, one for each group, in K
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 2.0
compressibility = 4.5e-5
ref_p   = 1.0
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = Protein
pull_group1 = LIG
pull_rate1  = 0.004  ; 0.004 nm per ps = 4 nm per ns
pull_k1 = 500  ; kJ mol^-1 nm^-2

I run 3 pulling simulations with the same mdp  and I obtain 3
different profiles (Force vs time). Then I used 2xlonger pulling with
the same pulling distance and I run 3 simulations again. Each time I
obtain different profile. Can anyone explain me this? I am using
velocities from npt simulation as above (gen_vel = no and continuation
= yes) so I presume the output should be similar. Please, advice.



I assume you're passing a checkpoint file to grompp?  If you're relying on 
velocities from the .gro file, they are of insufficient precision to guarantee 
proper continuation.


Small variations are inherent in any simulation set, and in the case of pulling, 
small changes (though intentional) are the basis for Jarzynski's method.  In any 
case, all MD simulations are chaotic and so it depends on what your definition 
of "different" is in the context of whether or not there are meaningful changes 
imparted through the course of each simulation.  Also note that in the absence 
of the -reprod flag, the same .tpr file may result in a slightly different 
outcome.  The implications of these outcomes are limited by sampling; the 
ensemble should converge with sufficient time and/or replicates.  For 
non-equilibrium processes like pulling, convergence is probably harder, but 
again you have to ask whether the differences are meaningful.


http://www.gromacs.org/Documentation/Terminology/Reproducibility

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] Pulling ligand - Different Profiles (Force vs time)

[Steven Neumann]

On Wed, Jun 27, 2012 at 1:51 PM, Justin A. Lemkul  wrote:
>
>
> On 6/27/12 7:48 AM, Steven Neumann wrote:
>>
>> Dear Gmx Users,
>>
>> I obtained a protein-ligand complex from 100ns simulation. Now I am
>> pulling my ligand away from the protein after the energy minimzation
>> in water and equilibration of 100ps (two coupling baths: Protein,
>> LIG_Water_and_ions).
>> Then I proceed my pulling :
>>
>> grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o
>> pull.tpr
>>
>> mdrun -s pull.tpr -deffnm pull
>>
>>
>> title       = Umbrella pulling simulation
>> define      = -DPOSRES
>> ; Run parameters
>> integrator  = md
>> dt          = 0.002
>> tinit       = 0
>> nsteps      = 50    ; 1 ns
>> nstcomm     = 10
>> ; Output parameters
>> nstxout     = 0
>> nstvout     = 0
>> nstfout     = 500
>> nstxtcout   = 1000       ; every 1 ps
>> nstenergy   = 500
>> ; Bond parameters
>> constraint_algorithm    = lincs
>> constraints             = all-bonds
>> continuation            = yes       ; continuing from NPT
>> ; Single-range cutoff scheme
>> nstlist     = 5
>> ns_type     = grid
>> rlist       = 1.4
>> rcoulomb    = 1.4
>> rvdw        = 1.2
>> vdwtype     = Switch
>> rvdw-switch = 1.0
>> ; PME electrostatics parameters
>> coulombtype     = PME
>> fourierspacing  = 0.12
>> fourier_nx      = 0
>> fourier_ny      = 0
>> fourier_nz      = 0
>> pme_order       = 4
>> ewald_rtol      = 1e-5
>> optimize_fft    = yes
>> ; Temperature coupling is on
>> tcoupl      = V-rescale                                  ; modified
>> Berendsen thermostat
>> tc_grps     = Protein LIG_Water_and_ions   ; two coupling groups - more
>> accurate
>> tau_t       = 0.1   0.1                                 ; time constant,
>> in ps
>> ref_t       = 298   298                                  ; reference
>> temperature, one for each group, in K
>> ; Pressure coupling is on
>> Pcoupl          = Parrinello-Rahman
>> pcoupltype      = isotropic
>> tau_p           = 2.0
>> compressibility = 4.5e-5
>> ref_p           = 1.0
>> ; Generate velocities is off
>> gen_vel     = no
>> ; Periodic boundary conditions are on in all directions
>> pbc     = xyz
>> ; Long-range dispersion correction
>> DispCorr    = EnerPres
>> ; Pull code
>> pull            = umbrella
>> pull_geometry   = distance  ; simple distance increase
>> pull_dim        = N N Y
>> pull_start      = yes       ; define initial COM distance > 0
>> pull_ngroups    = 1
>> pull_group0     = Protein
>> pull_group1     = LIG
>> pull_rate1      = 0.004      ; 0.004 nm per ps = 4 nm per ns
>> pull_k1         = 500      ; kJ mol^-1 nm^-2
>>
>> I run 3 pulling simulations with the same mdp  and I obtain 3
>> different profiles (Force vs time). Then I used 2xlonger pulling with
>> the same pulling distance and I run 3 simulations again. Each time I
>> obtain different profile. Can anyone explain me this? I am using
>> velocities from npt simulation as above (gen_vel = no and continuation
>> = yes) so I presume the output should be similar. Please, advice.
>>
>
> I assume you're passing a checkpoint file to grompp?  If you're relying on
> velocities from the .gro file, they are of insufficient precision to
> guarantee proper continuation.

Thank you Justin. I am using according to your tutorial:

grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr
mdrun -s pull.tpr -deffnm pull

Would you suggest:

grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr
mdrun -s pull.tpr -cpi npt.cpt -deffnm pull ??

Profiles do not vary slightly - the maximum pulling force (breaking
point) varies from 290 to 500 kJ/mol nm2 which is really a lot.

Steven

>
> Small variations are inherent in any simulation set, and in the case of
> pulling, small changes (though intentional) are the basis for Jarzynski's
> method.  In any case, all MD simulations are chaotic and so it depends on
> what your definition of "different" is in the context of whether or not
> there are meaningful changes imparted through the course of each simulation.
>  Also note that in the absence of the -reprod flag, the same .tpr file may
> result in a slightly different outcome.  The implications of these outcomes
> are limited by sampling; the ensemble should converge with sufficient time
> and/or replicates.  For non-equilibrium processes like pulling, convergence
> is probably harder, but again you have to ask whether the differences are
> meaningful.
>
> http://www.gromacs.org/Documentation/Terminology/Reproducibility
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!

Re: [gmx-users] Pulling ligand - Different Profiles (Force vs time)

[Justin A. Lemkul]

On 6/27/12 9:36 AM, Steven Neumann wrote:

On Wed, Jun 27, 2012 at 1:51 PM, Justin A. Lemkul  wrote:



On 6/27/12 7:48 AM, Steven Neumann wrote:


Dear Gmx Users,

I obtained a protein-ligand complex from 100ns simulation. Now I am
pulling my ligand away from the protein after the energy minimzation
in water and equilibration of 100ps (two coupling baths: Protein,
LIG_Water_and_ions).
Then I proceed my pulling :

grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o
pull.tpr

mdrun -s pull.tpr -deffnm pull


title   = Umbrella pulling simulation
define  = -DPOSRES
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 50; 1 ns
nstcomm = 10
; Output parameters
nstxout = 0
nstvout = 0
nstfout = 500
nstxtcout   = 1000   ; every 1 ps
nstenergy   = 500
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes   ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.2
vdwtype = Switch
rvdw-switch = 1.0
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Temperature coupling is on
tcoupl  = V-rescale  ; modified
Berendsen thermostat
tc_grps = Protein LIG_Water_and_ions   ; two coupling groups - more
accurate
tau_t   = 0.1   0.1 ; time constant,
in ps
ref_t   = 298   298  ; reference
temperature, one for each group, in K
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 2.0
compressibility = 4.5e-5
ref_p   = 1.0
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = Protein
pull_group1 = LIG
pull_rate1  = 0.004  ; 0.004 nm per ps = 4 nm per ns
pull_k1 = 500  ; kJ mol^-1 nm^-2

I run 3 pulling simulations with the same mdp  and I obtain 3
different profiles (Force vs time). Then I used 2xlonger pulling with
the same pulling distance and I run 3 simulations again. Each time I
obtain different profile. Can anyone explain me this? I am using
velocities from npt simulation as above (gen_vel = no and continuation
= yes) so I presume the output should be similar. Please, advice.



I assume you're passing a checkpoint file to grompp?  If you're relying on
velocities from the .gro file, they are of insufficient precision to
guarantee proper continuation.


Thank you Justin. I am using according to your tutorial:

grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr
mdrun -s pull.tpr -deffnm pull

Would you suggest:

grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr
mdrun -s pull.tpr -cpi npt.cpt -deffnm pull ??



No, I would not, especially if the NPT run uses position restraints, in which 
case the two phases are different.  I missed the command line in the earlier 
message.  What you are doing makes sense.



Profiles do not vary slightly - the maximum pulling force (breaking
point) varies from 290 to 500 kJ/mol nm2 which is really a lot.



Consult the points below and watch your trajectories.  If you're getting 
different forces, your ligands are experiencing different interactions.  SMD is 
a path-dependent, non-equilibrium process.  Good sampling and a justifiable path 
are key.


-Justin



Small variations are inherent in any simulation set, and in the case of
pulling, small changes (though intentional) are the basis for Jarzynski's
method.  In any case, all MD simulations are chaotic and so it depends on
what your definition of "different" is in the context of whether or not
there are meaningful changes imparted through the course of each simulation.
  Also note that in the absence of the -reprod flag, the same .tpr file may
result in a slightly different outcome.  The implications of these outcomes
are limited by sampling; the ensemble should converge with sufficient time
and/or replicates.  For non-equilibrium processes like pulling, convergence
is probably harder, but again you have to ask whether the differences are
meaningful.

http://www.gromacs.org/Documentation/Terminology/Reproducibility

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

===

Re: [gmx-users] H-atoms in .hdb file

[Shima Arasteh]

 
Anyway, thanks for your reply .
I appreciate you.

 Sincerely,
Shima

Sincerely,
Shima



From: Justin A. Lemkul 
To: Discussion list for GROMACS users  
Sent: Wednesday, June 27, 2012 3:54 PM
Subject: Re: [gmx-users] H-atoms in .hdb file



On 6/27/12 6:38 AM, Shima Arasteh wrote:
>
>
> I added this line to the residuetypes.dat file:
> FOR   Protein
>
> Then running this command:
> pdb2gmx -f protein.pdb -water spc -ter
>
> Written as blow:
>
> Processing chain 1 (177 atoms, 25 residues)
> Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA.
> Identified residue VAL1 as a starting terminus.
> Identified residue GLY24 as a ending terminus.
>
> Asked for terminus:
> I chose "none" as the N-terminus.
>
> Getting this:
>   Processing chain 1 (177 atoms, 25 residues)
> Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA.
> Identified residue VAL1 as a starting terminus.
> Identified residue GLY24 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Select start terminus type for VAL-1
>   0: NH3+
>   1: NH2
>   2: None
> 2
> Start terminus VAL-1: None
> Select end terminus type for GLY-24
>   0: COO-
>   1: COOH
>   2: None
> 0
> End terminus GLY-24: COO-
>
> ---
> Program pdb2gmx, VERSION 4.5.5
> Source code file: 
> /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/pdb2top.c, line: 1035
>
> Fatal error:
> There is a dangling bond at at least one of the terminal ends. Select a 
> proper terminal entry.
>
>
> Would you helping me with it with your useful suggestions?
>

I honestly have no idea why that's not working.  It's the exact same workflow 
used with all other capping groups and I use it routinely.

-Justin

-- 


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] Pulling ligand - Different Profiles (Force vs time)

[Steven Neumann]

Thank you Justin.

On Wed, Jun 27, 2012 at 2:39 PM, Justin A. Lemkul  wrote:
>
>
> On 6/27/12 9:36 AM, Steven Neumann wrote:
>>
>> On Wed, Jun 27, 2012 at 1:51 PM, Justin A. Lemkul  wrote:
>>>
>>>
>>>
>>> On 6/27/12 7:48 AM, Steven Neumann wrote:


 Dear Gmx Users,

 I obtained a protein-ligand complex from 100ns simulation. Now I am
 pulling my ligand away from the protein after the energy minimzation
 in water and equilibration of 100ps (two coupling baths: Protein,
 LIG_Water_and_ions).
 Then I proceed my pulling :

 grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o
 pull.tpr

 mdrun -s pull.tpr -deffnm pull


 title       = Umbrella pulling simulation
 define      = -DPOSRES
 ; Run parameters
 integrator  = md
 dt          = 0.002
 tinit       = 0
 nsteps      = 50    ; 1 ns
 nstcomm     = 10
 ; Output parameters
 nstxout     = 0
 nstvout     = 0
 nstfout     = 500
 nstxtcout   = 1000       ; every 1 ps
 nstenergy   = 500
 ; Bond parameters
 constraint_algorithm    = lincs
 constraints             = all-bonds
 continuation            = yes       ; continuing from NPT
 ; Single-range cutoff scheme
 nstlist     = 5
 ns_type     = grid
 rlist       = 1.4
 rcoulomb    = 1.4
 rvdw        = 1.2
 vdwtype     = Switch
 rvdw-switch = 1.0
 ; PME electrostatics parameters
 coulombtype     = PME
 fourierspacing  = 0.12
 fourier_nx      = 0
 fourier_ny      = 0
 fourier_nz      = 0
 pme_order       = 4
 ewald_rtol      = 1e-5
 optimize_fft    = yes
 ; Temperature coupling is on
 tcoupl      = V-rescale                                  ; modified
 Berendsen thermostat
 tc_grps     = Protein LIG_Water_and_ions   ; two coupling groups - more
 accurate
 tau_t       = 0.1   0.1                                 ; time constant,
 in ps
 ref_t       = 298   298                                  ; reference
 temperature, one for each group, in K
 ; Pressure coupling is on
 Pcoupl          = Parrinello-Rahman
 pcoupltype      = isotropic
 tau_p           = 2.0
 compressibility = 4.5e-5
 ref_p           = 1.0
 ; Generate velocities is off
 gen_vel     = no
 ; Periodic boundary conditions are on in all directions
 pbc     = xyz
 ; Long-range dispersion correction
 DispCorr    = EnerPres
 ; Pull code
 pull            = umbrella
 pull_geometry   = distance  ; simple distance increase
 pull_dim        = N N Y
 pull_start      = yes       ; define initial COM distance > 0
 pull_ngroups    = 1
 pull_group0     = Protein
 pull_group1     = LIG
 pull_rate1      = 0.004      ; 0.004 nm per ps = 4 nm per ns
 pull_k1         = 500      ; kJ mol^-1 nm^-2

 I run 3 pulling simulations with the same mdp  and I obtain 3
 different profiles (Force vs time). Then I used 2xlonger pulling with
 the same pulling distance and I run 3 simulations again. Each time I
 obtain different profile. Can anyone explain me this? I am using
 velocities from npt simulation as above (gen_vel = no and continuation
 = yes) so I presume the output should be similar. Please, advice.

>>>
>>> I assume you're passing a checkpoint file to grompp?  If you're relying
>>> on
>>> velocities from the .gro file, they are of insufficient precision to
>>> guarantee proper continuation.
>>
>>
>> Thank you Justin. I am using according to your tutorial:
>>
>> grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o
>> pull.tpr
>> mdrun -s pull.tpr -deffnm pull
>>
>> Would you suggest:
>>
>> grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o
>> pull.tpr
>> mdrun -s pull.tpr -cpi npt.cpt -deffnm pull ??
>>
>
> No, I would not, especially if the NPT run uses position restraints, in
> which case the two phases are different.  I missed the command line in the
> earlier message.  What you are doing makes sense.
>
>
>> Profiles do not vary slightly - the maximum pulling force (breaking
>> point) varies from 290 to 500 kJ/mol nm2 which is really a lot.
>>
>
> Consult the points below and watch your trajectories.  If you're getting
> different forces, your ligands are experiencing different interactions.  SMD
> is a path-dependent, non-equilibrium process.  Good sampling and a
> justifiable path are key.
>
> -Justin
>
>
>>>
>>> Small variations are inherent in any simulation set, and in the case of
>>> pulling, small changes (though intentional) are the basis for Jarzynski's
>>> method.  In any case, all MD simulations are chaotic and so it depends on
>>> what your definition of "different" is in the context of whether or not
>>> there are meaningful changes imparted through the course of each
>>> simulation.
>>>  Also note that in the absence of the -reprod flag, the same .tpr fi

[gmx-users] make index

[reisingere]

Hi everybody,
I want to  make an index with "make_ndx".

But when I just wanted to group SOL and CL   and   Protein and DPPC  it
tells me when I want to run grompp afterwards that there are some residues
not indexed.
I thought that that might be because the NA-ions are not grouped. But when
I want to group them together with the SOL and the CL with the command
14|15|17 and run grompp afterwards it tells me that the index SOL_Cl could
not be found. That is reasonable since my group is called: NA_CL_SOL
So my question is: how can I rename such a index group?

Bests, Eva

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Re: [gmx-users] make index

[Justin A. Lemkul]

On 6/27/12 11:08 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Hi everybody,
I want to  make an index with "make_ndx".

But when I just wanted to group SOL and CL   and   Protein and DPPC  it
tells me when I want to run grompp afterwards that there are some residues
not indexed.


Copying and pasting an error message is much more effective.  I could guess at 
what this error is, but seeing it would be more useful.



I thought that that might be because the NA-ions are not grouped. But when
I want to group them together with the SOL and the CL with the command
14|15|17 and run grompp afterwards it tells me that the index SOL_Cl could
not be found. That is reasonable since my group is called: NA_CL_SOL
So my question is: how can I rename such a index group?



The names specified in the .mdp file and .ndx files must match, so you can 
either change the names in the .mdp file (easiest), use a text editor to modify 
the name of the group in the .ndx file (same principle, probably a little more 
scrolling and/or find and replace), or use make_ndx to rename the groups (not 
very efficient in this case).


-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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[gmx-users] pdb2gmx error

[Shima Arasteh]

 Hi all,

I got this error :
Atom CA is used in an interaction of type improper in the topology database, 
but an atom of that name was not found in residue number 2.
I checked the pdb file and rtp file. 
.rtp file:
[ SER ]
 [ atoms ]
 N N  -0.280 0
 H H   0.280 0
    CA   CH1   0.000 1
    CB   CH2   0.150 2
    OG    OA  -0.548 2
    HG    HO   0.398 2
 C C   0.380 3
 O O  -0.380 3

.pdb file:

 ATOM 10  N   SER 2  -3.181   3.235   3.442 
ATOM 11  CA  SER 2  -3.363   4.671   3.524 
ATOM 12  C   SER 2  -4.135   5.054   4.778 
ATOM 13  O   SER 2  -5.272   4.628   4.966 
ATOM 14  CB  SER 2  -4.138   5.196   2.320 
ATOM 15  OG  SER 2  -4.296   6.612   2.437

I guess they are in agreement, so what's the problem?




Sincerely,
Shima
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[gmx-users] Re: pdb2gmx error

[shounakb]

Hi,
   C and O should be atoms 14 and 15 (i.e. the last two atoms)

Hope this works!
Shima Arasteh wrote
> 
>  Hi all,
> 
> I got this error :
> Atom CA is used in an interaction of type improper in the topology
> database, but an atom of that name was not found in residue number 2.
> I checked the pdb file and rtp file. 
> .rtp file:
> [ SER ]
>  [ atoms ]
>  N N  -0.280 0
>  H H   0.280 0
>     CA   CH1   0.000 1
>     CB   CH2   0.150 2
>     OG    OA  -0.548 2
>     HG    HO   0.398 2
>  C C   0.380 3
>  O O  -0.380 3
> 
> .pdb file:
> 
>  ATOM 10  N   SER 2  -3.181   3.235   3.442 
> ATOM 11  CA  SER 2  -3.363   4.671   3.524 
> ATOM 12  C   SER 2  -4.135   5.054   4.778 
> ATOM 13  O   SER 2  -5.272   4.628   4.966 
> ATOM 14  CB  SER 2  -4.138   5.196   2.320 
> ATOM 15  OG  SER 2  -4.296   6.612   2.437
> 
> I guess they are in agreement, so what's the problem?
> 
> 
> 
> 
> Sincerely,
> Shima
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[gmx-users] Re: pdb2gmx error

[shounakb]

Hi,
   C and O should go last (i.e. their atom numbers should be 14 and 15
respectively.
Hope this works!

Regards,
Shounak

Shima Arasteh wrote
> 
>  Hi all,
> 
> I got this error :
> Atom CA is used in an interaction of type improper in the topology
> database, but an atom of that name was not found in residue number 2.
> I checked the pdb file and rtp file. 
> .rtp file:
> [ SER ]
>  [ atoms ]
>  N N  -0.280 0
>  H H   0.280 0
>     CA   CH1   0.000 1
>     CB   CH2   0.150 2
>     OG    OA  -0.548 2
>     HG    HO   0.398 2
>  C C   0.380 3
>  O O  -0.380 3
> 
> .pdb file:
> 
>  ATOM 10  N   SER 2  -3.181   3.235   3.442 
> ATOM 11  CA  SER 2  -3.363   4.671   3.524 
> ATOM 12  C   SER 2  -4.135   5.054   4.778 
> ATOM 13  O   SER 2  -5.272   4.628   4.966 
> ATOM 14  CB  SER 2  -4.138   5.196   2.320 
> ATOM 15  OG  SER 2  -4.296   6.612   2.437
> 
> I guess they are in agreement, so what's the problem?
> 
> 
> 
> 
> Sincerely,
> Shima
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Re: [gmx-users] Re: pdb2gmx error

[Shima Arasteh]

You mean the order of C and O should be changed in .pdb file? If yes, it didn't 
work!

 
Sincerely,
Shima


- Original Message -
From: shounakb 
To: gmx-users@gromacs.org
Cc: 
Sent: Wednesday, June 27, 2012 8:39 PM
Subject: [gmx-users] Re: pdb2gmx error

Hi,
   C and O should go last (i.e. their atom numbers should be 14 and 15
respectively.
Hope this works!

Regards,
Shounak

Shima Arasteh wrote
> 
>  Hi all,
> 
> I got this error :
> Atom CA is used in an interaction of type improper in the topology
> database, but an atom of that name was not found in residue number 2.
> I checked the pdb file and rtp file. 
> .rtp file:
> [ SER ]
>  [ atoms ]
>  N N  -0.280 0
>  H H   0.280 0
>     CA   CH1   0.000 1
>     CB   CH2   0.150 2
>     OG    OA  -0.548 2
>     HG    HO   0.398 2
>  C C   0.380 3
>  O O  -0.380 3
> 
> .pdb file:
> 
>  ATOM 10  N   SER 2  -3.181   3.235   3.442 
> ATOM 11  CA  SER 2  -3.363   4.671   3.524 
> ATOM 12  C   SER 2  -4.135   5.054   4.778 
> ATOM 13  O   SER 2  -5.272   4.628   4.966 
> ATOM 14  CB  SER 2  -4.138   5.196   2.320 
> ATOM 15  OG  SER 2  -4.296   6.612   2.437
> 
> I guess they are in agreement, so what's the problem?
> 
> 
> 
> 
> Sincerely,
> Shima
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Re: [gmx-users] Re: pdb2gmx error

[Justin A. Lemkul]

On 6/27/12 12:25 PM, Shima Arasteh wrote:

You mean the order of C and O should be changed in .pdb file? If yes, it didn't 
work!



The order of atoms in the .pdb file is irrelevant.  What may be the issue is 
that when pdb2gmx is reporting the error, it is printing its own internal 
residue number (i.e., the second residue in the chain) - are you missing residue 
1?  Files downloaded from the PDB are also convenient because they report all 
missing atoms with "MISSING" entries in the header of the file.  These entries 
will indicate problems before even running pdb2gmx.


-Justin



Sincerely,
Shima


- Original Message -
From: shounakb 
To: gmx-users@gromacs.org
Cc:
Sent: Wednesday, June 27, 2012 8:39 PM
Subject: [gmx-users] Re: pdb2gmx error

Hi,
C and O should go last (i.e. their atom numbers should be 14 and 15
respectively.
Hope this works!

Regards,
Shounak

Shima Arasteh wrote


  Hi all,

I got this error :
Atom CA is used in an interaction of type improper in the topology
database, but an atom of that name was not found in residue number 2.
I checked the pdb file and rtp file.
.rtp file:
[ SER ]
  [ atoms ]
  N N  -0.280 0
  H H   0.280 0
 CA   CH1   0.000 1
 CB   CH2   0.150 2
 OGOA  -0.548 2
 HGHO   0.398 2
  C C   0.380 3
  O O  -0.380 3

.pdb file:

  ATOM 10  N   SER 2  -3.181   3.235   3.442
ATOM 11  CA  SER 2  -3.363   4.671   3.524
ATOM 12  C   SER 2  -4.135   5.054   4.778
ATOM 13  O   SER 2  -5.272   4.628   4.966
ATOM 14  CB  SER 2  -4.138   5.196   2.320
ATOM 15  OG  SER 2  -4.296   6.612   2.437

I guess they are in agreement, so what's the problem?




Sincerely,
Shima
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--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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[gmx-users] tabulated potentials and soft core free energy - this should not work ....

[Michael Brunsteiner]

Hi,

i meant to perform a free energy calculation to get the chemical
potential of water, and made a number of input files based on the excellent 
tutorial
by Justin Lemkul.
(Without thinking) I also tried using a tabulated potential for electrostatics
with: coulombtype = User
but it seems to work - all the numbers in dhdl.xvg are finite and non-zero, and 
neither mdrun nor
grompp give me a warning) 
but then it shouldn't work ... how is Gromacs supposed to calculate the 
dU/dlambda term ?
or Is this calculated numerically?
or did i overlook something here?
below my mdp file

thanks for any advice!

michael



mdp:


integrator   = sd
nsteps   = 10
dt   = 0.002
;
pbc  = xyz
nstcomm  = 100
comm_grps    = System
;
nstxtcout    =
0
nstenergy    = 100
nst_log  = 0
nstxout  = 0
nstvout  = 0
;
rlist    = 1.35
;
coulombtype  = User
rcoulomb = 1.2
vdw-type =
switch
rvdw-switch  = 1.0
rvdw = 1.2
;
tc_grps  = system
tau_t    = 1.0
ref_t    = 300
;
Pcoupl   = Berendsen
tau_p    = 0.5
compressibility  =
4.5e-5
ref_p    = 1.0
pcoupltype   = isotropic
;
constraints  = hbonds
lincs_iter   = 8
;
free_energy  = yes
init_lambda  = 0.50
delta_lambda = 0
foreign_lambda   = 0.40 0.60
dhdl_derivatives =
yes
sc_alpha = 0.5
sc_power = 1
sc_sigma = 0.5
nstdhdl  = 100
couple-moltype   = w1
couple-lambda0   = vdw-q
couple-lambda1   = none
couple-intramol  = no



===
Why be happy when you could be normal?
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Re: [gmx-users] Re: pdb2gmx error

[Shima Arasteh]

I know that no missing atom is here.
As the fatal error is about atom name CA, I checked it, but it's actually 
existed in both .rtp and pdb in agreement.
Please help me, I don't know what to do :(

 
Sincerely,
Shima


- Original Message -
From: Justin A. Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc: 
Sent: Wednesday, June 27, 2012 8:58 PM
Subject: Re: [gmx-users] Re: pdb2gmx error



On 6/27/12 12:25 PM, Shima Arasteh wrote:
> You mean the order of C and O should be changed in .pdb file? If yes, it 
> didn't work!
>

The order of atoms in the .pdb file is irrelevant.  What may be the issue is 
that when pdb2gmx is reporting the error, it is printing its own internal 
residue number (i.e., the second residue in the chain) - are you missing 
residue 
1?  Files downloaded from the PDB are also convenient because they report all 
missing atoms with "MISSING" entries in the header of the file.  These entries 
will indicate problems before even running pdb2gmx.

-Justin

>
> Sincerely,
> Shima
>
>
> - Original Message -
> From: shounakb 
> To: gmx-users@gromacs.org
> Cc:
> Sent: Wednesday, June 27, 2012 8:39 PM
> Subject: [gmx-users] Re: pdb2gmx error
>
> Hi,
>     C and O should go last (i.e. their atom numbers should be 14 and 15
> respectively.
> Hope this works!
>
> Regards,
> Shounak
>
> Shima Arasteh wrote
>>
>>   Hi all,
>>
>> I got this error :
>> Atom CA is used in an interaction of type improper in the topology
>> database, but an atom of that name was not found in residue number 2.
>> I checked the pdb file and rtp file.
>> .rtp file:
>> [ SER ]
>>   [ atoms ]
>>       N     N  -0.280     0
>>       H     H   0.280     0
>>      CA   CH1   0.000     1
>>      CB   CH2   0.150     2
>>      OG    OA  -0.548     2
>>      HG    HO   0.398     2
>>       C     C   0.380     3
>>       O     O  -0.380     3
>>
>> .pdb file:
>>
>>   ATOM     10  N   SER     2      -3.181   3.235   3.442
>> ATOM     11  CA  SER     2      -3.363   4.671   3.524
>> ATOM     12  C   SER     2      -4.135   5.054   4.778
>> ATOM     13  O   SER     2      -5.272   4.628   4.966
>> ATOM     14  CB  SER     2      -4.138   5.196   2.320
>> ATOM     15  OG  SER     2      -4.296   6.612   2.437
>>
>> I guess they are in agreement, so what's the problem?
>>
>>
>>
>>
>> Sincerely,
>> Shima
>> --
>> gmx-users mailing list    gmx-users@
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Only plain text messages are allowed!
>> * Please search the archive at
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>>
>
>
> --
> View this message in context: 
> http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998848.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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-- 


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Re: pdb2gmx error

[Justin A. Lemkul]

On 6/27/12 12:43 PM, Shima Arasteh wrote:

I know that no missing atom is here.
As the fatal error is about atom name CA, I checked it, but it's actually 
existed in both .rtp and pdb in agreement.
Please help me, I don't know what to do :(



Please copy and paste the entirety of the first three residues in your .pdb file 
so we can see what you're working with.


-Justin



Sincerely,
Shima


- Original Message -
From: Justin A. Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS users 

Cc:
Sent: Wednesday, June 27, 2012 8:58 PM
Subject: Re: [gmx-users] Re: pdb2gmx error



On 6/27/12 12:25 PM, Shima Arasteh wrote:

You mean the order of C and O should be changed in .pdb file? If yes, it didn't 
work!



The order of atoms in the .pdb file is irrelevant.  What may be the issue is
that when pdb2gmx is reporting the error, it is printing its own internal
residue number (i.e., the second residue in the chain) - are you missing residue
1?  Files downloaded from the PDB are also convenient because they report all
missing atoms with "MISSING" entries in the header of the file.  These entries
will indicate problems before even running pdb2gmx.

-Justin



Sincerely,
Shima


- Original Message -
From: shounakb 
To: gmx-users@gromacs.org
Cc:
Sent: Wednesday, June 27, 2012 8:39 PM
Subject: [gmx-users] Re: pdb2gmx error

Hi,
  C and O should go last (i.e. their atom numbers should be 14 and 15
respectively.
Hope this works!

Regards,
Shounak

Shima Arasteh wrote


Hi all,

I got this error :
Atom CA is used in an interaction of type improper in the topology
database, but an atom of that name was not found in residue number 2.
I checked the pdb file and rtp file.
.rtp file:
[ SER ]
[ atoms ]
N N  -0.280 0
H H   0.280 0
   CA   CH1   0.000 1
   CB   CH2   0.150 2
   OGOA  -0.548 2
   HGHO   0.398 2
C C   0.380 3
O O  -0.380 3

.pdb file:

ATOM 10  N   SER 2  -3.181   3.235   3.442
ATOM 11  CA  SER 2  -3.363   4.671   3.524
ATOM 12  C   SER 2  -4.135   5.054   4.778
ATOM 13  O   SER 2  -5.272   4.628   4.966
ATOM 14  CB  SER 2  -4.138   5.196   2.320
ATOM 15  OG  SER 2  -4.296   6.612   2.437

I guess they are in agreement, so what's the problem?




Sincerely,
Shima
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View this message in context: 
http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998848.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] Re: pdb2gmx error

[Shima Arasteh]

OK.
 PDB FILE IS AS BELOW:

HETATM    1  C   FOR 0  -0.721   1.600   1.249 
HETATM    2  O   FOR 0  -0.839   2.806   1.453 
ATOM  3  N   VAL 1  -1.227   0.728   2.125 
ATOM  4  CA  VAL 1  -1.918   1.159   3.323 
ATOM  5  C   VAL 1  -1.969   2.678   3.410 
ATOM  6  O   VAL 1  -0.931   3.335   3.447 
ATOM  7  CB  VAL 1  -1.219   0.644   4.576 
ATOM  8  CG1 VAL 1   0.208   1.178   4.618 
ATOM  9  CG2 VAL 1  -1.976   1.118   5.812 
ATOM 10  N   SER 2  -3.181   3.235   3.442 
ATOM 11  CA  SER 2  -3.363   4.671   3.524 
ATOM 12  CB  SER 2  -4.138   5.196   2.320 
ATOM 13  OG  SER 2  -4.296   6.612   2.437 
ATOM 14  C   SER 2  -4.135   5.054   4.778 
ATOM 15  O   SER 2  -5.272   4.628   4.966

 
Sincerely,
Shima


- Original Message -
From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Wednesday, June 27, 2012 9:14 PM
Subject: Re: [gmx-users] Re: pdb2gmx error



On 6/27/12 12:43 PM, Shima Arasteh wrote:
> I know that no missing atom is here.
> As the fatal error is about atom name CA, I checked it, but it's actually 
> existed in both .rtp and pdb in agreement.
> Please help me, I don't know what to do :(
>

Please copy and paste the entirety of the first three residues in your .pdb 
file 
so we can see what you're working with.

-Justin

>
> Sincerely,
> Shima
>
>
> - Original Message -
> From: Justin A. Lemkul 
> To: Shima Arasteh ; Discussion list for GROMACS 
> users 
> Cc:
> Sent: Wednesday, June 27, 2012 8:58 PM
> Subject: Re: [gmx-users] Re: pdb2gmx error
>
>
>
> On 6/27/12 12:25 PM, Shima Arasteh wrote:
>> You mean the order of C and O should be changed in .pdb file? If yes, it 
>> didn't work!
>>
>
> The order of atoms in the .pdb file is irrelevant.  What may be the issue is
> that when pdb2gmx is reporting the error, it is printing its own internal
> residue number (i.e., the second residue in the chain) - are you missing 
> residue
> 1?  Files downloaded from the PDB are also convenient because they report all
> missing atoms with "MISSING" entries in the header of the file.  These entries
> will indicate problems before even running pdb2gmx.
>
> -Justin
>
>>
>> Sincerely,
>> Shima
>>
>>
>> - Original Message -
>> From: shounakb 
>> To: gmx-users@gromacs.org
>> Cc:
>> Sent: Wednesday, June 27, 2012 8:39 PM
>> Subject: [gmx-users] Re: pdb2gmx error
>>
>> Hi,
>>       C and O should go last (i.e. their atom numbers should be 14 and 15
>> respectively.
>> Hope this works!
>>
>> Regards,
>> Shounak
>>
>> Shima Arasteh wrote
>>>
>>>     Hi all,
>>>
>>> I got this error :
>>> Atom CA is used in an interaction of type improper in the topology
>>> database, but an atom of that name was not found in residue number 2.
>>> I checked the pdb file and rtp file.
>>> .rtp file:
>>> [ SER ]
>>>     [ atoms ]
>>>         N     N  -0.280     0
>>>         H     H   0.280     0
>>>        CA   CH1   0.000     1
>>>        CB   CH2   0.150     2
>>>        OG    OA  -0.548     2
>>>        HG    HO   0.398     2
>>>         C     C   0.380     3
>>>         O     O  -0.380     3
>>>
>>> .pdb file:
>>>
>>>     ATOM     10  N   SER     2      -3.181   3.235   3.442
>>> ATOM     11  CA  SER     2      -3.363   4.671   3.524
>>> ATOM     12  C   SER     2      -4.135   5.054   4.778
>>> ATOM     13  O   SER     2      -5.272   4.628   4.966
>>> ATOM     14  CB  SER     2      -4.138   5.196   2.320
>>> ATOM     15  OG  SER     2      -4.296   6.612   2.437
>>>
>>> I guess they are in agreement, so what's the problem?
>>>
>>>
>>>
>>>
>>> Sincerely,
>>> Shima
>>> --
>>> gmx-users mailing list    gmx-users@
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Only plain text messages are allowed!
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request@.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>> --
>> View this message in context: 
>> http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998848.html
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Only plain text messages are allowed!
>> * Please search the archive at 
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>> www interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 23

[gmx-users] Re: pdb2gmx error

[shounakb]

Hi,
   removing the HETATMs worked for me when i used AMBER99SB's rtp file.
What force field are you using? Have you added the FOR topology manually (I
know this is besides the point about the problem with serine) AMBER99SB
seemed to only have topology for acetate [ACE]
I am also learning through this.
Sincerely,
Shounak

Shima Arasteh wrote
> 
> OK.
>  PDB FILE IS AS BELOW:
> 
> HETATM    1  C   FOR 0  -0.721   1.600   1.249 
> HETATM    2  O   FOR 0  -0.839   2.806   1.453 
> ATOM  3  N   VAL 1  -1.227   0.728   2.125 
> ATOM  4  CA  VAL 1  -1.918   1.159   3.323 
> ATOM  5  C   VAL 1  -1.969   2.678   3.410 
> ATOM  6  O   VAL 1  -0.931   3.335   3.447 
> ATOM  7  CB  VAL 1  -1.219   0.644   4.576 
> ATOM  8  CG1 VAL 1   0.208   1.178   4.618 
> ATOM  9  CG2 VAL 1  -1.976   1.118   5.812 
> ATOM 10  N   SER 2  -3.181   3.235   3.442 
> ATOM 11  CA  SER 2  -3.363   4.671   3.524 
> ATOM 12  CB  SER 2  -4.138   5.196   2.320 
> ATOM 13  OG  SER 2  -4.296   6.612   2.437 
> ATOM 14  C   SER 2  -4.135   5.054   4.778 
> ATOM 15  O   SER 2  -5.272   4.628   4.966
> 
>  
> Sincerely,
> Shima
> 
> 
> - Original Message -
> From: Justin A. Lemkul 
> To: Discussion list for GROMACS users 
> Cc: 
> Sent: Wednesday, June 27, 2012 9:14 PM
> Subject: Re: [gmx-users] Re: pdb2gmx error
> 
> 
> 
> On 6/27/12 12:43 PM, Shima Arasteh wrote:
>> I know that no missing atom is here.
>> As the fatal error is about atom name CA, I checked it, but it's actually
>> existed in both .rtp and pdb in agreement.
>> Please help me, I don't know what to do :(
>>
> 
> Please copy and paste the entirety of the first three residues in your
> .pdb file 
> so we can see what you're working with.
> 
> -Justin
> 
>>
>> Sincerely,
>> Shima
>>
>>
>> - Original Message -
>> From: Justin A. Lemkul 
>> To: Shima Arasteh ; Discussion list for GROMACS
>> users 
>> Cc:
>> Sent: Wednesday, June 27, 2012 8:58 PM
>> Subject: Re: [gmx-users] Re: pdb2gmx error
>>
>>
>>
>> On 6/27/12 12:25 PM, Shima Arasteh wrote:
>>> You mean the order of C and O should be changed in .pdb file? If yes, it
>>> didn't work!
>>>
>>
>> The order of atoms in the .pdb file is irrelevant.  What may be the issue
>> is
>> that when pdb2gmx is reporting the error, it is printing its own internal
>> residue number (i.e., the second residue in the chain) - are you missing
>> residue
>> 1?  Files downloaded from the PDB are also convenient because they report
>> all
>> missing atoms with "MISSING" entries in the header of the file.  These
>> entries
>> will indicate problems before even running pdb2gmx.
>>
>> -Justin
>>
>>>
>>> Sincerely,
>>> Shima
>>>
>>>
>>> - Original Message -
>>> From: shounakb 
>>> To: gmx-users@
>>> Cc:
>>> Sent: Wednesday, June 27, 2012 8:39 PM
>>> Subject: [gmx-users] Re: pdb2gmx error
>>>
>>> Hi,
>>>       C and O should go last (i.e. their atom numbers should be 14 and
15
>>> respectively.
>>> Hope this works!
>>>
>>> Regards,
>>> Shounak
>>>
>>> Shima Arasteh wrote

     Hi all,

 I got this error :
 Atom CA is used in an interaction of type improper in the topology
 database, but an atom of that name was not found in residue number 2.
 I checked the pdb file and rtp file.
 .rtp file:
 [ SER ]
     [ atoms ]
         N     N  -0.280     0
         H     H   0.280     0
        CA   CH1   0.000     1
        CB   CH2   0.150     2
        OG    OA  -0.548     2
        HG    HO   0.398     2
         C     C   0.380     3
         O     O  -0.380     3

 .pdb file:

     ATOM     10  N   SER     2      -3.181   3.235   3.442
 ATOM     11  CA  SER     2      -3.363   4.671   3.524
 ATOM     12  C   SER     2      -4.135   5.054   4.778
 ATOM     13  O   SER     2      -5.272   4.628   4.966
 ATOM     14  CB  SER     2      -4.138   5.196   2.320
 ATOM     15  OG  SER     2      -4.296   6.612   2.437

 I guess they are in agreement, so what's the problem?




 Sincerely,
 Shima
 --
 gmx-users mailing list    gmx-users@
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 * Only plain text messages are allowed!
 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 * Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-request@.
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>>>
>>>
>>> --
>>> View this message in context:
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Re: [gmx-users] Re: pdb2gmx error

[Shima Arasteh]

If I remove HETATMs, then what about the FOR residue?
Thanks for your suggestions.

 
Sincerely,
Shima


- Original Message -
From: shounakb 
To: gmx-users@gromacs.org
Cc: 
Sent: Wednesday, June 27, 2012 9:42 PM
Subject: [gmx-users] Re: pdb2gmx error

Hi,
   removing the HETATMs worked for me when i used AMBER99SB's rtp file.
What force field are you using? Have you added the FOR topology manually (I
know this is besides the point about the problem with serine) AMBER99SB
seemed to only have topology for acetate [ACE]
I am also learning through this.
Sincerely,
Shounak

Shima Arasteh wrote
> 
> OK.
>  PDB FILE IS AS BELOW:
> 
> HETATM    1  C   FOR 0  -0.721   1.600   1.249 
> HETATM    2  O   FOR 0  -0.839   2.806   1.453 
> ATOM  3  N   VAL 1  -1.227   0.728   2.125 
> ATOM  4  CA  VAL 1  -1.918   1.159   3.323 
> ATOM  5  C   VAL 1  -1.969   2.678   3.410 
> ATOM  6  O   VAL 1  -0.931   3.335   3.447 
> ATOM  7  CB  VAL 1  -1.219   0.644   4.576 
> ATOM  8  CG1 VAL 1   0.208   1.178   4.618 
> ATOM  9  CG2 VAL 1  -1.976   1.118   5.812 
> ATOM 10  N   SER 2  -3.181   3.235   3.442 
> ATOM 11  CA  SER 2  -3.363   4.671   3.524 
> ATOM 12  CB  SER 2  -4.138   5.196   2.320 
> ATOM 13  OG  SER 2  -4.296   6.612   2.437 
> ATOM 14  C   SER 2  -4.135   5.054   4.778 
> ATOM 15  O   SER 2  -5.272   4.628   4.966
> 
>  
> Sincerely,
> Shima
> 
> 
> - Original Message -
> From: Justin A. Lemkul 
> To: Discussion list for GROMACS users 
> Cc: 
> Sent: Wednesday, June 27, 2012 9:14 PM
> Subject: Re: [gmx-users] Re: pdb2gmx error
> 
> 
> 
> On 6/27/12 12:43 PM, Shima Arasteh wrote:
>> I know that no missing atom is here.
>> As the fatal error is about atom name CA, I checked it, but it's actually
>> existed in both .rtp and pdb in agreement.
>> Please help me, I don't know what to do :(
>>
> 
> Please copy and paste the entirety of the first three residues in your
> .pdb file 
> so we can see what you're working with.
> 
> -Justin
> 
>>
>> Sincerely,
>> Shima
>>
>>
>> - Original Message -
>> From: Justin A. Lemkul 
>> To: Shima Arasteh ; Discussion list for GROMACS
>> users 
>> Cc:
>> Sent: Wednesday, June 27, 2012 8:58 PM
>> Subject: Re: [gmx-users] Re: pdb2gmx error
>>
>>
>>
>> On 6/27/12 12:25 PM, Shima Arasteh wrote:
>>> You mean the order of C and O should be changed in .pdb file? If yes, it
>>> didn't work!
>>>
>>
>> The order of atoms in the .pdb file is irrelevant.  What may be the issue
>> is
>> that when pdb2gmx is reporting the error, it is printing its own internal
>> residue number (i.e., the second residue in the chain) - are you missing
>> residue
>> 1?  Files downloaded from the PDB are also convenient because they report
>> all
>> missing atoms with "MISSING" entries in the header of the file.  These
>> entries
>> will indicate problems before even running pdb2gmx.
>>
>> -Justin
>>
>>>
>>> Sincerely,
>>> Shima
>>>
>>>
>>> - Original Message -
>>> From: shounakb 
>>> To: gmx-users@
>>> Cc:
>>> Sent: Wednesday, June 27, 2012 8:39 PM
>>> Subject: [gmx-users] Re: pdb2gmx error
>>>
>>> Hi,
>>>       C and O should go last (i.e. their atom numbers should be 14 and
15
>>> respectively.
>>> Hope this works!
>>>
>>> Regards,
>>> Shounak
>>>
>>> Shima Arasteh wrote

     Hi all,

 I got this error :
 Atom CA is used in an interaction of type improper in the topology
 database, but an atom of that name was not found in residue number 2.
 I checked the pdb file and rtp file.
 .rtp file:
 [ SER ]
     [ atoms ]
         N     N  -0.280     0
         H     H   0.280     0
        CA   CH1   0.000     1
        CB   CH2   0.150     2
        OG    OA  -0.548     2
        HG    HO   0.398     2
         C     C   0.380     3
         O     O  -0.380     3

 .pdb file:

     ATOM     10  N   SER     2      -3.181   3.235   3.442
 ATOM     11  CA  SER     2      -3.363   4.671   3.524
 ATOM     12  C   SER     2      -4.135   5.054   4.778
 ATOM     13  O   SER     2      -5.272   4.628   4.966
 ATOM     14  CB  SER     2      -4.138   5.196   2.320
 ATOM     15  OG  SER     2      -4.296   6.612   2.437

 I guess they are in agreement, so what's the problem?




 Sincerely,
 Shima
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Re: [gmx-users] Re: pdb2gmx error

[Justin A. Lemkul]

On 6/27/12 12:50 PM, Shima Arasteh wrote:

OK.
  PDB FILE IS AS BELOW:

HETATM1  C   FOR 0  -0.721   1.600   1.249
HETATM2  O   FOR 0  -0.839   2.806   1.453
ATOM  3  N   VAL 1  -1.227   0.728   2.125
ATOM  4  CA  VAL 1  -1.918   1.159   3.323
ATOM  5  C   VAL 1  -1.969   2.678   3.410
ATOM  6  O   VAL 1  -0.931   3.335   3.447
ATOM  7  CB  VAL 1  -1.219   0.644   4.576
ATOM  8  CG1 VAL 1   0.208   1.178   4.618
ATOM  9  CG2 VAL 1  -1.976   1.118   5.812
ATOM 10  N   SER 2  -3.181   3.235   3.442
ATOM 11  CA  SER 2  -3.363   4.671   3.524
ATOM 12  CB  SER 2  -4.138   5.196   2.320
ATOM 13  OG  SER 2  -4.296   6.612   2.437
ATOM 14  C   SER 2  -4.135   5.054   4.778
ATOM 15  O   SER 2  -5.272   4.628   4.966




The error comes from the VAL residue (residue 2 in the sequence based on the 
internal numbering used by pdb2gmx, as I suspected earlier).  Note the following 
line in the [impropers] section of aminoacids.rtp in the [VAL] entry:


   -C   -CA N-O

The improper is defined using the position of a CA atom in the preceding 
residue, which in this case does not exist because it is not a normal amino acid 
(though an ACE cap will also work because its atoms are named suitably).  This 
method of defining the improper is somewhat odd.  Using a more modern force 
field like Gromos96 53a6 does not give rise to this error, as all impropers are 
defined using only -C or +N.  Just another reason to use a non-deprecated force 
field :)


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] Re: pdb2gmx error

[Shima Arasteh]

I know it's much better to use a non-deprecated ff.  But what could I do? I 
have to regenerate the results of simulation done by gmx.ff . Aren't there any 
solution to pass this step? 

I PROMISE YOU AND ME TO REPEAT THE SIMULATION WHIT A MODERN FF AS SOON AS 
POSSIBLE :)

 
Sincerely,
Shima


- Original Message -
From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Wednesday, June 27, 2012 9:55 PM
Subject: Re: [gmx-users] Re: pdb2gmx error



On 6/27/12 12:50 PM, Shima Arasteh wrote:
> OK.
>   PDB FILE IS AS BELOW:
> 
> HETATM    1  C   FOR     0      -0.721   1.600   1.249
> HETATM    2  O   FOR     0      -0.839   2.806   1.453
> ATOM      3  N   VAL     1      -1.227   0.728   2.125
> ATOM      4  CA  VAL     1      -1.918   1.159   3.323
> ATOM      5  C   VAL     1      -1.969   2.678   3.410
> ATOM      6  O   VAL     1      -0.931   3.335   3.447
> ATOM      7  CB  VAL     1      -1.219   0.644   4.576
> ATOM      8  CG1 VAL     1       0.208   1.178   4.618
> ATOM      9  CG2 VAL     1      -1.976   1.118   5.812
> ATOM     10  N   SER     2      -3.181   3.235   3.442
> ATOM     11  CA  SER     2      -3.363   4.671   3.524
> ATOM     12  CB  SER     2      -4.138   5.196   2.320
> ATOM     13  OG  SER     2      -4.296   6.612   2.437
> ATOM     14  C   SER     2      -4.135   5.054   4.778
> ATOM     15  O   SER     2      -5.272   4.628   4.966
> 
> 

The error comes from the VAL residue (residue 2 in the sequence based on the 
internal numbering used by pdb2gmx, as I suspected earlier).  Note the 
following line in the [impropers] section of aminoacids.rtp in the [VAL] entry:

   -C   -CA     N    -O

The improper is defined using the position of a CA atom in the preceding 
residue, which in this case does not exist because it is not a normal amino 
acid (though an ACE cap will also work because its atoms are named suitably).  
This method of defining the improper is somewhat odd.  Using a more modern 
force field like Gromos96 53a6 does not give rise to this error, as all 
impropers are defined using only -C or +N.  Just another reason to use a 
non-deprecated force field :)

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] Re: pdb2gmx error

[Justin A. Lemkul]

On 6/27/12 1:35 PM, Shima Arasteh wrote:

I know it's much better to use a non-deprecated ff.  But what could I do? I 
have to regenerate the results of simulation done by gmx.ff . Aren't there any 
solution to pass this step?


I have no idea how to make gmx.ff work.  I "solved" the issue by commenting out 
the line and seeing that no error resulted.  This, of course, isn't an actual 
solution, just a debugging method.  The force field defines its impropers in an 
odd way, and as such I don't know that there is a workaround.




I PROMISE YOU AND ME TO REPEAT THE SIMULATION WHIT A MODERN FF AS SOON AS 
POSSIBLE :)



The sooner, the better.  This is an ancient force field, and vastly better 
parameter sets exist.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] Re: pdb2gmx error

[Shima Arasteh]

Dear Justin,
Again, I appreciate you. I learn much from you, feeling happy :)

Thanks a lot.

 
Sincerely,
Shima


- Original Message -
From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Wednesday, June 27, 2012 10:10 PM
Subject: Re: [gmx-users] Re: pdb2gmx error



On 6/27/12 1:35 PM, Shima Arasteh wrote:
> I know it's much better to use a non-deprecated ff.  But what could I do? I 
> have to regenerate the results of simulation done by gmx.ff . Aren't there 
> any solution to pass this step?

I have no idea how to make gmx.ff work.  I "solved" the issue by commenting out 
the line and seeing that no error resulted.  This, of course, isn't an actual 
solution, just a debugging method.  The force field defines its impropers in an 
odd way, and as such I don't know that there is a workaround.

> 
> I PROMISE YOU AND ME TO REPEAT THE SIMULATION WHIT A MODERN FF AS SOON AS 
> POSSIBLE :)
> 

The sooner, the better.  This is an ancient force field, and vastly better 
parameter sets exist.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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[gmx-users] Re: pdb2gmx error

[shounakb]

Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp
file works fine for the sequence you originally specified. (pdb2gmx executes
without any errors)
I guess you added the FOR cap's topology yourself?

Justin, could this be an issue?

Sincerely,
Shounak

--
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Re: [gmx-users] Re: pdb2gmx error

[Justin A. Lemkul]

On 6/27/12 1:52 PM, shounakb wrote:

Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp
file works fine for the sequence you originally specified. (pdb2gmx executes
without any errors)
I guess you added the FOR cap's topology yourself?

Justin, could this be an issue?



Please see the previous posts on these topics, including the post from just a 
few minutes ago where I discovered the source of the problem.  The FOR residue 
issue has been an ongoing discussion over several weeks.  I will maintain that I 
do not necessarily believe that a two-atom model of a formyl group is 
sufficiently accurate for a Gromos force field, since the alpha proton is very 
polar and thus may need to be explicitly represented.  I have stated my 
skepticism before but it appears Shima is pursuing the current course.  Side note ;)


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] Re: pdb2gmx error

[Shima Arasteh]

Dear Shounak,
So what's about the FOR residue? I can't eliminate it. I guess if I do as you 
suggest, I need to add the FOR to n.tdb and then the procedure would be 
different!
Yes, I added the FOR to rtp file on my own.

 
Sincerely,
Shima


- Original Message -
From: shounakb 
To: gmx-users@gromacs.org
Cc: 
Sent: Wednesday, June 27, 2012 10:22 PM
Subject: [gmx-users] Re: pdb2gmx error

Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp
file works fine for the sequence you originally specified. (pdb2gmx executes
without any errors)
I guess you added the FOR cap's topology yourself?

Justin, could this be an issue?

Sincerely,
Shounak

--
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Re: [gmx-users] Re: pdb2gmx error

[Justin A. Lemkul]

On 6/27/12 1:58 PM, Shima Arasteh wrote:

Dear Shounak,
So what's about the FOR residue? I can't eliminate it. I guess if I do as you 
suggest, I need to add the FOR to n.tdb and then the procedure would be 
different!


You do not need to add FOR to a .tdb entry.  These directives are only to modify 
protonation states of amines and carboxylates.  I believe you tried this before, 
and my comment was that such a procedure would not work (and it didn't).


-Justin


Yes, I added the FOR to rtp file on my own.


Sincerely,
Shima


- Original Message -
From: shounakb 
To: gmx-users@gromacs.org
Cc:
Sent: Wednesday, June 27, 2012 10:22 PM
Subject: [gmx-users] Re: pdb2gmx error

Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp
file works fine for the sequence you originally specified. (pdb2gmx executes
without any errors)
I guess you added the FOR cap's topology yourself?

Justin, could this be an issue?

Sincerely,
Shounak

--
View this message in context: 
http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998861.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.



--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] Re: pdb2gmx error

[Shima Arasteh]

:))
I can't eliminate it, I decided to do , but when I studied about the structure 
of protein ( consists of 2 monomers, which form a dimer in lipid bilayer, and 
the reason of this formation is the existence of formyl residues in N-teminals) 
. Then I got regretful to remove it. Don't you agree?

 
Sincerely,
Shima


- Original Message -
From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Wednesday, June 27, 2012 10:25 PM
Subject: Re: [gmx-users] Re: pdb2gmx error



On 6/27/12 1:52 PM, shounakb wrote:
> Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp
> file works fine for the sequence you originally specified. (pdb2gmx executes
> without any errors)
> I guess you added the FOR cap's topology yourself?
> 
> Justin, could this be an issue?
> 

Please see the previous posts on these topics, including the post from just a 
few minutes ago where I discovered the source of the problem.  The FOR residue 
issue has been an ongoing discussion over several weeks.  I will maintain that 
I do not necessarily believe that a two-atom model of a formyl group is 
sufficiently accurate for a Gromos force field, since the alpha proton is very 
polar and thus may need to be explicitly represented.  I have stated my 
skepticism before but it appears Shima is pursuing the current course.  Side 
note ;)

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] Re: pdb2gmx error

[Justin A. Lemkul]

On 6/27/12 2:05 PM, Shima Arasteh wrote:

:)) I can't eliminate it, I decided to do , but when I studied about the
structure of protein ( consists of 2 monomers, which form a dimer in lipid
bilayer, and the reason of this formation is the existence of formyl residues
in N-teminals) . Then I got regretful to remove it. Don't you agree?




The decision should not be whether or not there is an N-formylation on your 
protein.  It seems obvious that you need it.  The real issue is how it is 
represented, which entails two issues:


1. A parent force field to use
2. Parameterization of the formyl group under the rules of the parent force 
field

The mechanics within Gromacs are irrelevant to these concerns and only matter 
once those points are satisfied.  No matter the force field you choose, the 
assembly of the topology through pdb2gmx is the same.


-Justin


Sincerely, Shima


- Original Message - From: Justin A. Lemkul  To:
Discussion list for GROMACS users  Cc: Sent:
Wednesday, June 27, 2012 10:25 PM Subject: Re: [gmx-users] Re: pdb2gmx error



On 6/27/12 1:52 PM, shounakb wrote:

Shima, I use gromacs-4.5.4. Without the FOR residue, my
gmx.ff/aminoacids.rtp file works fine for the sequence you originally
specified. (pdb2gmx executes without any errors) I guess you added the FOR
cap's topology yourself?

Justin, could this be an issue?



Please see the previous posts on these topics, including the post from just a
few minutes ago where I discovered the source of the problem.  The FOR
residue issue has been an ongoing discussion over several weeks.  I will
maintain that I do not necessarily believe that a two-atom model of a formyl
group is sufficiently accurate for a Gromos force field, since the alpha
proton is very polar and thus may need to be explicitly represented.  I have
stated my skepticism before but it appears Shima is pursuing the current
course.  Side note ;)

-Justin

-- 

Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry
Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] Re: pdb2gmx error

[Shima Arasteh]

So as you said it doesn't matter to remove the FOR residue. But I can't 
understand why the representation of FOR is still required!

And,  you suggest me to use another forcefield to produce the topology and then 
go on whit it by gmx ? Would I need to maintain the FOR in the new FF or 
eliminate it? Honestly I'm a little confused here.


 
Sincerely,
Shima


- Original Message -
From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Wednesday, June 27, 2012 10:39 PM
Subject: Re: [gmx-users] Re: pdb2gmx error



On 6/27/12 2:05 PM, Shima Arasteh wrote:
> :)) I can't eliminate it, I decided to do , but when I studied about the
> structure of protein ( consists of 2 monomers, which form a dimer in lipid
> bilayer, and the reason of this formation is the existence of formyl residues
> in N-teminals) . Then I got regretful to remove it. Don't you agree?
>
>

The decision should not be whether or not there is an N-formylation on your 
protein.  It seems obvious that you need it.  The real issue is how it is 
represented, which entails two issues:

1. A parent force field to use
2. Parameterization of the formyl group under the rules of the parent force 
field

The mechanics within Gromacs are irrelevant to these concerns and only matter 
once those points are satisfied.  No matter the force field you choose, the 
assembly of the topology through pdb2gmx is the same.

-Justin

> Sincerely, Shima
>
>
> - Original Message - From: Justin A. Lemkul  To:
> Discussion list for GROMACS users  Cc: Sent:
> Wednesday, June 27, 2012 10:25 PM Subject: Re: [gmx-users] Re: pdb2gmx error
>
>
>
> On 6/27/12 1:52 PM, shounakb wrote:
>> Shima, I use gromacs-4.5.4. Without the FOR residue, my
>> gmx.ff/aminoacids.rtp file works fine for the sequence you originally
>> specified. (pdb2gmx executes without any errors) I guess you added the FOR
>> cap's topology yourself?
>>
>> Justin, could this be an issue?
>>
>
> Please see the previous posts on these topics, including the post from just a
> few minutes ago where I discovered the source of the problem.  The FOR
> residue issue has been an ongoing discussion over several weeks.  I will
> maintain that I do not necessarily believe that a two-atom model of a formyl
> group is sufficiently accurate for a Gromos force field, since the alpha
> proton is very polar and thus may need to be explicitly represented.  I have
> stated my skepticism before but it appears Shima is pursuing the current
> course.  Side note ;)
>
> -Justin
>
> -- 
>
> Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry
> Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
>
> -- gmx-users mailing list    gmx-users@gromacs.org
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> messages are allowed! * Please search the archive at
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>
>

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] Re: pdb2gmx error

[Justin A. Lemkul]

On 6/27/12 2:23 PM, Shima Arasteh wrote:

So as you said it doesn't matter to remove the FOR residue. But I can't
understand why the representation of FOR is still required!



I did not say that.  Your last message gave the reason why the formyl group is 
necessary.  Have I misunderstood?  This is all getting really confusing.  If 
you're adding a formyl cap, then you'd better have a reason for it, otherwise 
all of this is a grand waste of time.



And,  you suggest me to use another forcefield to produce the topology and
then go on whit it by gmx ? Would I need to maintain the FOR in the new FF or
eliminate it? Honestly I'm a little confused here.



Yes, you should use a more reliable force field.  You should choose it based on 
significant reading about the pros and cons of different force fields and what 
people generally use to simulate similar systems.  You will then need to 
re-derive parameters for the formyl group based on the parameterization 
methodology required by the force field.


-Justin




Sincerely, Shima


- Original Message - From: Justin A. Lemkul  To:
Discussion list for GROMACS users  Cc: Sent:
Wednesday, June 27, 2012 10:39 PM Subject: Re: [gmx-users] Re: pdb2gmx error



On 6/27/12 2:05 PM, Shima Arasteh wrote:

:)) I can't eliminate it, I decided to do , but when I studied about the
structure of protein ( consists of 2 monomers, which form a dimer in lipid
bilayer, and the reason of this formation is the existence of formyl
residues in N-teminals) . Then I got regretful to remove it. Don't you
agree?




The decision should not be whether or not there is an N-formylation on your
protein.  It seems obvious that you need it.  The real issue is how it is
represented, which entails two issues:

1. A parent force field to use 2. Parameterization of the formyl group under
the rules of the parent force field

The mechanics within Gromacs are irrelevant to these concerns and only
matter once those points are satisfied.  No matter the force field you
choose, the assembly of the topology through pdb2gmx is the same.

-Justin


Sincerely, Shima


- Original Message - From: Justin A. Lemkul  To:
Discussion list for GROMACS users  Cc: Sent:
Wednesday, June 27, 2012 10:25 PM Subject: Re: [gmx-users] Re: pdb2gmx
error



On 6/27/12 1:52 PM, shounakb wrote:

Shima, I use gromacs-4.5.4. Without the FOR residue, my
gmx.ff/aminoacids.rtp file works fine for the sequence you originally
specified. (pdb2gmx executes without any errors) I guess you added the
FOR cap's topology yourself?

Justin, could this be an issue?



Please see the previous posts on these topics, including the post from just
a few minutes ago where I discovered the source of the problem.  The FOR
residue issue has been an ongoing discussion over several weeks.  I will
maintain that I do not necessarily believe that a two-atom model of a
formyl group is sufficiently accurate for a Gromos force field, since the
alpha proton is very polar and thus may need to be explicitly represented.
I have stated my skepticism before but it appears Shima is pursuing the
current course.  Side note ;)

-Justin

-- 

Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry
Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




-- gmx-users mailing listgmx-users@gromacs.org
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messages are allowed! * Please search the archive at
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or send it to gmx-users-requ...@gromacs.org. * Can't post? Read
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--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] Re: pdb2gmx error

[Shima Arasteh]

You are right. 

OK, the reason of adding FOR is what I explained a few minutes ago.
All over, I'm supposed to use a modern FF . ( In similar researches I found 
CHARMM is suitable, so I would add FOR as the procedure explained in 
GROMACS.ORG) 

For now, because I wanna regenerate an old simulation, I keep the FOR, then 
here it's stopped! Seeking for a solution!

If any suggestion, I look forward hearing from you.
THANKS FOR ALL YOUR KIND REPLIES! :)

 
Sincerely,
Shima


- Original Message -
From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Wednesday, June 27, 2012 10:58 PM
Subject: Re: [gmx-users] Re: pdb2gmx error



On 6/27/12 2:23 PM, Shima Arasteh wrote:
> So as you said it doesn't matter to remove the FOR residue. But I can't
> understand why the representation of FOR is still required!
>

I did not say that.  Your last message gave the reason why the formyl group is 
necessary.  Have I misunderstood?  This is all getting really confusing.  If 
you're adding a formyl cap, then you'd better have a reason for it, otherwise 
all of this is a grand waste of time.

> And,  you suggest me to use another forcefield to produce the topology and
> then go on whit it by gmx ? Would I need to maintain the FOR in the new FF or
> eliminate it? Honestly I'm a little confused here.
>

Yes, you should use a more reliable force field.  You should choose it based on 
significant reading about the pros and cons of different force fields and what 
people generally use to simulate similar systems.  You will then need to 
re-derive parameters for the formyl group based on the parameterization 
methodology required by the force field.

-Justin

>
>
> Sincerely, Shima
>
>
> - Original Message - From: Justin A. Lemkul  To:
> Discussion list for GROMACS users  Cc: Sent:
> Wednesday, June 27, 2012 10:39 PM Subject: Re: [gmx-users] Re: pdb2gmx error
>
>
>
> On 6/27/12 2:05 PM, Shima Arasteh wrote:
>> :)) I can't eliminate it, I decided to do , but when I studied about the
>> structure of protein ( consists of 2 monomers, which form a dimer in lipid
>> bilayer, and the reason of this formation is the existence of formyl
>> residues in N-teminals) . Then I got regretful to remove it. Don't you
>> agree?
>>
>>
>
> The decision should not be whether or not there is an N-formylation on your
> protein.  It seems obvious that you need it.  The real issue is how it is
> represented, which entails two issues:
>
> 1. A parent force field to use 2. Parameterization of the formyl group under
> the rules of the parent force field
>
> The mechanics within Gromacs are irrelevant to these concerns and only
> matter once those points are satisfied.  No matter the force field you
> choose, the assembly of the topology through pdb2gmx is the same.
>
> -Justin
>
>> Sincerely, Shima
>>
>>
>> - Original Message - From: Justin A. Lemkul  To:
>> Discussion list for GROMACS users  Cc: Sent:
>> Wednesday, June 27, 2012 10:25 PM Subject: Re: [gmx-users] Re: pdb2gmx
>> error
>>
>>
>>
>> On 6/27/12 1:52 PM, shounakb wrote:
>>> Shima, I use gromacs-4.5.4. Without the FOR residue, my
>>> gmx.ff/aminoacids.rtp file works fine for the sequence you originally
>>> specified. (pdb2gmx executes without any errors) I guess you added the
>>> FOR cap's topology yourself?
>>>
>>> Justin, could this be an issue?
>>>
>>
>> Please see the previous posts on these topics, including the post from just
>> a few minutes ago where I discovered the source of the problem.  The FOR
>> residue issue has been an ongoing discussion over several weeks.  I will
>> maintain that I do not necessarily believe that a two-atom model of a
>> formyl group is sufficiently accurate for a Gromos force field, since the
>> alpha proton is very polar and thus may need to be explicitly represented.
>> I have stated my skepticism before but it appears Shima is pursuing the
>> current course.  Side note ;)
>>
>> -Justin
>>
>> -- 
>>
>> Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry
>> Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>>
>>
>> -- gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text
>> messages are allowed! * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! *
>> Please don't post (un)subscribe requests to the list. Use the www interface
>> or send it to gmx-users-requ...@gromacs.org. * Can't post? Read
>> http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




-- 

[gmx-users] Re: pdb2gmx error

[shounakb]

Hi Shima,
i do not think pdb2gmx uses the tdb files. However, I feel that the FOR
tdb entries should go to aminoacids.c.tdb and not aminoacids.n.tdb

I saw your other thread where you have described the FOR topology you added.
I think the atoms should be CA and O and their respective atom types,
CH1/CH2 and O.

I guess you already have partial charges for the atoms? Shouldn't that solve
the problem with VAL that Justin highlighted, without having to comment out
the impropers line?

Regards,
Shounak


Shima Arasteh wrote
> 
> :))
> I can't eliminate it, I decided to do , but when I studied about the
> structure of protein ( consists of 2 monomers, which form a dimer in lipid
> bilayer, and the reason of this formation is the existence of formyl
> residues in N-teminals) . Then I got regretful to remove it. Don't you
> agree?
> 
>  
> Sincerely,
> Shima
> 
> 
> - Original Message -
> From: Justin A. Lemkul 
> To: Discussion list for GROMACS users 
> Cc: 
> Sent: Wednesday, June 27, 2012 10:25 PM
> Subject: Re: [gmx-users] Re: pdb2gmx error
> 
> 
> 
> On 6/27/12 1:52 PM, shounakb wrote:
>> Shima, I use gromacs-4.5.4. Without the FOR residue, my
>> gmx.ff/aminoacids.rtp
>> file works fine for the sequence you originally specified. (pdb2gmx
>> executes
>> without any errors)
>> I guess you added the FOR cap's topology yourself?
>> 
>> Justin, could this be an issue?
>> 
> 
> Please see the previous posts on these topics, including the post from
> just a few minutes ago where I discovered the source of the problem.  The
> FOR residue issue has been an ongoing discussion over several weeks.  I
> will maintain that I do not necessarily believe that a two-atom model of a
> formyl group is sufficiently accurate for a Gromos force field, since the
> alpha proton is very polar and thus may need to be explicitly
> represented.  I have stated my skepticism before but it appears Shima is
> pursuing the current course.  Side note ;)
> 
> -Justin
> 
> -- 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> 
> 
> -- gmx-users mailing list    gmx-users@
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> interface or send it to gmx-users-request@.
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> 
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Re: [gmx-users] Re: pdb2gmx error

[Justin A. Lemkul]

On 6/27/12 2:49 PM, shounakb wrote:

Hi Shima,
 i do not think pdb2gmx uses the tdb files. However, I feel that the FOR
tdb entries should go to aminoacids.c.tdb and not aminoacids.n.tdb



Both of these assertions are incorrect.  The *only* Gromacs program that uses 
.tdb files is pdb2gmx.  The FOR cap is on the N-terminus, so it cannot be in 
.c.tdb.  Both .tdb files are irrelevant for this problem, as stated before.



I saw your other thread where you have described the FOR topology you added.
I think the atoms should be CA and O and their respective atom types,
CH1/CH2 and O.



This does not solve the problem.  If one changes the "C" atom name to "CA" then 
pdb2gmx will certainly complain that the atom "C" is missing, since improper 
construction for VAL is dependent upon atoms "C" and "CA" being present in the 
preceding residue.



I guess you already have partial charges for the atoms? Shouldn't that solve
the problem with VAL that Justin highlighted, without having to comment out
the impropers line?



Partial charges are irrelevant here.  The error complains about an atom not 
being found, not the charge on any given atom.  Shima has a functional .rtp 
entry for the FOR residue.  It is not the problem, VAL is.  Better stated, the 
mechanism used by gmx.ff to generate impropers in this case blocks the use of 
FOR as a separate residue, since it does not contain the same atoms as an amino 
acid, specifically a C and CA.


-Justin


Regards,
Shounak


Shima Arasteh wrote


:))
I can't eliminate it, I decided to do , but when I studied about the
structure of protein ( consists of 2 monomers, which form a dimer in lipid
bilayer, and the reason of this formation is the existence of formyl
residues in N-teminals) . Then I got regretful to remove it. Don't you
agree?


Sincerely,
Shima


- Original Message -
From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Cc:
Sent: Wednesday, June 27, 2012 10:25 PM
Subject: Re: [gmx-users] Re: pdb2gmx error



On 6/27/12 1:52 PM, shounakb wrote:

Shima, I use gromacs-4.5.4. Without the FOR residue, my
gmx.ff/aminoacids.rtp
file works fine for the sequence you originally specified. (pdb2gmx
executes
without any errors)
I guess you added the FOR cap's topology yourself?

Justin, could this be an issue?



Please see the previous posts on these topics, including the post from
just a few minutes ago where I discovered the source of the problem.  The
FOR residue issue has been an ongoing discussion over several weeks.  I
will maintain that I do not necessarily believe that a two-atom model of a
formyl group is sufficiently accurate for a Gromos force field, since the
alpha proton is very polar and thus may need to be explicitly
represented.  I have stated my skepticism before but it appears Shima is
pursuing the current course.  Side note ;)

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] Re: pdb2gmx error

[Justin A. Lemkul]

On 6/27/12 2:42 PM, Shima Arasteh wrote:

You are right.

OK, the reason of adding FOR is what I explained a few minutes ago.
All over, I'm supposed to use a modern FF . ( In similar researches I found 
CHARMM is suitable, so I would add FOR as the procedure explained in 
GROMACS.ORG)



This sounds like a good idea.


For now, because I wanna regenerate an old simulation, I keep the FOR, then 
here it's stopped! Seeking for a solution!



There is one possible solution that I just thought of.  Rather than using FOR as 
its own residue, create a formylated valine, thus eliminating the problem with 
the call to CA of the preceding residue.


The .rtp entry:

[ FVAL ]
 [ atoms ]
CN   CH1   0.380 0
ON O  -0.380 0
 N N  -0.280 1
 H H   0.280 1
CA   CH1   0.000 2
CB   CH1   0.000 3
   CG1   CH3   0.000 4
   CG2   CH3   0.000 5
 C C   0.380 6
 O O  -0.380 6
 [ bonds ]
CNON
CN N
 N H
 NCA
CA C
 C O
CACB
CB   CG1
CB   CG2
 [ impropers ]
 NCNCA H
CN   -CA NON
CA N CCB
CB   CG2   CG1CA

The .hdb entry:

FVAL1
1   1   H   N   CN  CA

Then add FVAL to residuetypes.dat as a protein residue.  Processing the .pdb 
file you posted before (merging FOR and VAL into FVAL and adjusting names 
according to the .rtp entry above) works correctly.


Disclaimer: this method "works" (i.e. produces a topology) but I do not 
necessarily endorse the use of the parameters shown.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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[gmx-users] NVT, NPT and then pulling?

[Steven Neumann]

Dear Gmx Users,

I am wondering whether would you advise to run NVT, NPT (position
restrained) and before the pulling simulation e.g of the ligand from
protein-ligand complex? As I saw in Justin tutorial he equilibrate the
system with only NPT ensemble before pulling. Is that really sufficent
e.g. for 200 ps?

Thanks,

Steven
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Re: [gmx-users] NVT, NPT and then pulling?

[Justin A. Lemkul]

On 6/27/12 4:30 PM, Steven Neumann wrote:

Dear Gmx Users,

I am wondering whether would you advise to run NVT, NPT (position
restrained) and before the pulling simulation e.g of the ligand from
protein-ligand complex? As I saw in Justin tutorial he equilibrate the
system with only NPT ensemble before pulling. Is that really sufficent
e.g. for 200 ps?



There is no catch-all equilibration scheme that works universally.  NVT and NPT 
are commonly run in sequence.  My systems in the tutorial are quite robust and a 
single NPT phase is sufficient.  Please do not assume that this is universally 
true.  Your protocol should be based on how stable your systems are and how well 
your desired observables converge, but that much is true of every simulation.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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[gmx-users] Re: pdb2gmx error

[shounakb]

sorry about  the previous post! I have not yet looked at the code for pdb2gmx
(and a lot of other stuff).
I think the formyl-valine idea is pretty cool and found this thread very
informative.
Thank you!
Shounak

Justin A. Lemkul wrote
> 
> On 6/27/12 2:49 PM, shounakb wrote:
>> Hi Shima,
>>  i do not think pdb2gmx uses the tdb files. However, I feel that the
>> FOR
>> tdb entries should go to aminoacids.c.tdb and not aminoacids.n.tdb
>>
> 
> Both of these assertions are incorrect.  The *only* Gromacs program that
> uses 
> .tdb files is pdb2gmx.  The FOR cap is on the N-terminus, so it cannot be
> in 
> .c.tdb.  Both .tdb files are irrelevant for this problem, as stated
> before.
> 
>> I saw your other thread where you have described the FOR topology you
>> added.
>> I think the atoms should be CA and O and their respective atom types,
>> CH1/CH2 and O.
>>
> 
> This does not solve the problem.  If one changes the "C" atom name to "CA"
> then 
> pdb2gmx will certainly complain that the atom "C" is missing, since
> improper 
> construction for VAL is dependent upon atoms "C" and "CA" being present in
> the 
> preceding residue.
> 
>> I guess you already have partial charges for the atoms? Shouldn't that
>> solve
>> the problem with VAL that Justin highlighted, without having to comment
>> out
>> the impropers line?
>>
> 
> Partial charges are irrelevant here.  The error complains about an atom
> not 
> being found, not the charge on any given atom.  Shima has a functional
> .rtp 
> entry for the FOR residue.  It is not the problem, VAL is.  Better stated,
> the 
> mechanism used by gmx.ff to generate impropers in this case blocks the use
> of 
> FOR as a separate residue, since it does not contain the same atoms as an
> amino 
> acid, specifically a C and CA.
> 
> -Justin
> 
>> Regards,
>> Shounak
>>
>>
>> Shima Arasteh wrote
>>>
>>> :))
>>> I can't eliminate it, I decided to do , but when I studied about the
>>> structure of protein ( consists of 2 monomers, which form a dimer in
>>> lipid
>>> bilayer, and the reason of this formation is the existence of formyl
>>> residues in N-teminals) . Then I got regretful to remove it. Don't you
>>> agree?
>>>
>>>
>>> Sincerely,
>>> Shima
>>>
>>>
>>> - Original Message -
>>> From: Justin A. Lemkul 
>>> To: Discussion list for GROMACS users 
>>> Cc:
>>> Sent: Wednesday, June 27, 2012 10:25 PM
>>> Subject: Re: [gmx-users] Re: pdb2gmx error
>>>
>>>
>>>
>>> On 6/27/12 1:52 PM, shounakb wrote:
 Shima, I use gromacs-4.5.4. Without the FOR residue, my
 gmx.ff/aminoacids.rtp
 file works fine for the sequence you originally specified. (pdb2gmx
 executes
 without any errors)
 I guess you added the FOR cap's topology yourself?

 Justin, could this be an issue?

>>>
>>> Please see the previous posts on these topics, including the post from
>>> just a few minutes ago where I discovered the source of the problem. 
>>> The
>>> FOR residue issue has been an ongoing discussion over several weeks.  I
>>> will maintain that I do not necessarily believe that a two-atom model of
>>> a
>>> formyl group is sufficiently accurate for a Gromos force field, since
>>> the
>>> alpha proton is very polar and thus may need to be explicitly
>>> represented.  I have stated my skepticism before but it appears Shima is
>>> pursuing the current course.  Side note ;)
>>>
>>> -Justin
>>>
>>> -- 
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> 
>>>
>>>
>>> -- gmx-users mailing listgmx-users@
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>>>
>>
>>
>> --
>> View this message in context:
>> http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998870.html
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>>
> 
> -- 
> 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA

Re: [gmx-users] Re: pdb2gmx error

[Shima Arasteh]

Dear Justin,
All right. I'll give it a try. Thanks Justin.

I hope it works and the FOR issue would be terminated 


 
Sincerely,
Shima


- Original Message -
From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Thursday, June 28, 2012 12:17 AM
Subject: Re: [gmx-users] Re: pdb2gmx error



On 6/27/12 2:42 PM, Shima Arasteh wrote:
> You are right.
> 
> OK, the reason of adding FOR is what I explained a few minutes ago.
> All over, I'm supposed to use a modern FF . ( In similar researches I found 
> CHARMM is suitable, so I would add FOR as the procedure explained in 
> GROMACS.ORG)
> 

This sounds like a good idea.

> For now, because I wanna regenerate an old simulation, I keep the FOR, then 
> here it's stopped! Seeking for a solution!
> 

There is one possible solution that I just thought of.  Rather than using FOR 
as its own residue, create a formylated valine, thus eliminating the problem 
with the call to CA of the preceding residue.

The .rtp entry:

[ FVAL ]
[ atoms ]
    CN   CH1   0.380     0
    ON     O  -0.380     0
     N     N  -0.280     1
     H     H   0.280     1
    CA   CH1   0.000     2
    CB   CH1   0.000     3
   CG1   CH3   0.000     4
   CG2   CH3   0.000     5
     C     C   0.380     6
     O     O  -0.380     6
[ bonds ]
    CN    ON
    CN     N
     N     H
     N    CA
    CA     C
     C     O
    CA    CB
    CB   CG1
    CB   CG2
[ impropers ]
     N    CN    CA     H
    CN   -CA     N    ON
    CA     N     C    CB
    CB   CG2   CG1    CA

The .hdb entry:

FVAL    1
1   1   H   N   CN  CA

Then add FVAL to residuetypes.dat as a protein residue.  Processing the .pdb 
file you posted before (merging FOR and VAL into FVAL and adjusting names 
according to the .rtp entry above) works correctly.

Disclaimer: this method "works" (i.e. produces a topology) but I do not 
necessarily endorse the use of the parameters shown.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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