[gmx-users] regarding error in editconf

[Anamika Awasthi]

Dear friends

   when I am trying command editconf, it is showing error
File input/output error
  I have protein of 700 amino acids  and its of inverted T shape and we are
giving boxtype dodecahedron.

input command is:


 editconf_d -bt dodecahedron -f input.gro -o box.gro -c -d 10.0


with regards

Anamika
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RE: [gmx-users] charmm27 force filed bug for MET residue with vsites in gromacs 4.5.2

[Berk Hess]

Hi,

Note that grompp prints the atomtype that causes the problems.

You should copy the last line of share/top/charmm27.ff/gb.itp and rename MCH3 
to MCH3S.
I have fixed this for 4.5.3 and I have also made the grompp error messages 
clearer.

Berk

From: zhn...@gmail.com
To: gmx-users@gromacs.org
Date: Wed, 3 Nov 2010 21:23:33 -0700
Subject: [gmx-users] charmm27 force filed bug for MET residue with vsites in
gromacs 4.5.2 

Dear all:
I used gromacs 4.5.2 to generate the topology for a small protein with 
charmm27.pdb2gmx_mpi -f 1PIN.pdb -o protein.gro -vsite hydrogen -his -ignh -ter 
-p topol -nochargegrp
When I try to use the topology in grompp, the following error appeared: Fatal 
error:Can't do GB electrostatics; the forcefield is missing 1 values 
foratomtype radii, or they might be negative
I was able to isolate the atom that's causing the problem, which is MCH3S in 
the Met residue (as shown in the attached segment of the topology). It was 
named MCH3 as in gromacs 4.5.1. However, if I rename the atom, then another 
error occurs:  No default Constr. No Conn. types (between atom 181 and 182)
This problem does NOT show up in 4.5.1.
Thanks,Bin


   171NH1 15MET  N171  -0.47 15.015   ; qtot 
1.53172  H 15MET HN172   0.31  0   ; 
qtot 1.84173CT1 15MET CA173   0.07 13.019   
; qtot 1.91174 HB 15MET HA174   0.09  0 
  ; qtot 2   175CT2 15MET CB175  -0.18 14.027   
; qtot 1.82176 HA 15METHB1176   0.09  0 
  ; qtot 1.91177 HA 15METHB2177   0.09  
0   ; qtot 2   178CT2 15MET CG178  -0.14 14.027 
  ; qtot 1.86179 HA 15METHG1179   0.09  
0   ; qtot 1.95180 HA 15METHG2180   0.09
  0   ; qtot 2.04181  S 15MET SD181  -0.09  
32.06   ; qtot 1.95182  MCH3S 15MET   MCE1182  0
 7.5175   ; qtot 1.95183  MCH3S 15MET   MCE2183  0  
   7.5175   ; qtot 1.95184CT3 15MET CE184  
-0.22  0   ; qtot 1.73185 HA 15METHE1185
   0.09  0   ; qtot 1.82186 HA 15METHE2186  
 0.09  0   ; qtot 1.91187 HA 15METHE3
187   0.09  0   ; qtot 2   188  C 15MET  C
188   0.51 12.011   ; qtot 2.51189  O 15MET  O  
  189  -0.51 15.999   ; qtot 2

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[gmx-users] GB-polarization

[Christian Mücksch]

Dear all,

I've got a general question regarding implicit solvent simulations.
Using g_energy there's an option to print out the GB-polarization. Is 
that the solvent-solute electrostatics polarization free energy?


How can one interpret a rise or decrease in the GB-polarization?

Kind regards,

--
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Department of Physics
TU Kaiserslautern
Erwin Schrödinger Straße
67663 Kaiserslautern
Germany

Phone: +49 (0)631 205 4287
Email: mueck...@rhrk.uni-kl.de

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[gmx-users] g_sas resarea.xvg

[Carla Jamous]

Hi everyone,

I used g_sas: g_sas -s .tpr -f .xtc -n .ndx -o .xvg -or resarea.xvg

What I don't understand is why there are 3 columns in the file resarea.xvg
although this is what's written in my file:
# g_sas is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@title "Area per residue"
@xaxis  label "Residue"
@yaxis  label "Area (nm\S2\N)"
@TYPE xy

So I would expect this file to contain only two columns. I'm using gromacs
version 4.0.3.

Thanks for your help,
Carla
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Re: [gmx-users] g_hbond

[Carla Jamous]

Hi Erik,

I tried what you said: I made index groups containing only the atoms
involved in that hbond and ran g_hbond again. The problem didn't persist.
So I wanted to check if I misinterpreted the map: for that, I compared my 4
index files: the one of my concatenated trajectory and the three of the
separate trajectories.
When I look at this comparison table and then at my concatenated hbond map,
the results don't match: for example, the Hbond that has the number 1 in my
concatenated trajectory doesn't appear in my concatenated map (it means that
in my map, next to y=1, nothing appears), however, this same H-bond (same
number of atoms involved) exists in my first and my third trajectories'
index files. So please could you explain how to interpret the map and if
next to some y value in my map, nothing appears, is this value taken into
account in my index file?

Thank you,
Carla

On Tue, Nov 2, 2010 at 8:36 PM, Erik Marklund  wrote:

> Erik Marklund skrev 2010-11-02 20.33:
>
>  Carla Jamous skrev 2010-11-02 17.35:
>>
>>> Hi to all,
>>>
>>> I'm sorry I'm asking again a question I asked a week ago but I still
>>> haven't found my answer:
>>>
>>> I concatenated 3 trajectories of 3 different molecules (that have the
>>> same number of atoms) with trjcat: trjcat -settime
>>>
>>> Then I ran g_hbond on the concatenated trajectory, I got an index.ndx
>>> file that contains an H-bond between the Thr121 of my protein and an atom N2
>>> of my ligand. This H_bond  figures in the 3 trajectories when I look at the
>>> hbmap of my concatenated trajectory.
>>>
>>> On the other hand, I ran g_hbond on each of the 3 different trajectories.
>>> This H_bond doesn't exist in the index files of two of my trajectories. So
>>> it doesn't match the result I get with my concatenated trajectory.
>>>
>>> To be sure that this result is right, I calculated the angle and the r of
>>> my H-bond in VMD during each of the 3 trajectories and the results indicate
>>> that this H-bond doesn't exist (I consider that r must be < or equal to 0.35
>>> nm and angle < or equal to 30 degrees).
>>>
>>> Please can anyone tell me why the results of g_hbond in my concatenated
>>> trajectory don't match the results of g_hbond on each of my trajectories?
>>>
>>> Thank you
>>>
>>> Carla
>>>
>> Hi,
>>
>> This sounds strange. Could you file a bugzilla and either upload the
>> trajectories+tpr, or, if the files are huge, make them available my other
>> means? I need to have a closer look, perhaps through a debugger.
>>
>>  A simple test you could do yourself is to make index groups containing
> only the atoms involved in that hbond and run g_hbond again. If the problem
> persists, then it looks like a bug. If not, then I still can't rule out
> misinterpretation of the matrix.
>
> Erik
>
>
> --
> ---
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 4537fax: +46 18 511 755
> er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/
>
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Re: [gmx-users] regarding error in editconf

[Justin A. Lemkul]

Anamika Awasthi wrote:

Dear friends

   when I am trying command editconf, it is showing error
File input/output error
  I have protein of 700 amino acids  and its of inverted T shape and we 
are giving boxtype dodecahedron.


input command is:


 editconf_d -bt dodecahedron -f input.gro -o box.gro -c -d 10.0




If you're getting an I/O error, then either the input file doesn't exist or you 
don't have permission or sufficient disk space to write the output.  The full 
error message probably would have given more clues, but the reason likely falls 
into one of these categories.


-Justin


with regards

Anamika



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] g_sas resarea.xvg

[Justin A. Lemkul]

Carla Jamous wrote:

Hi everyone,

I used g_sas: g_sas -s .tpr -f .xtc -n .ndx -o .xvg -or resarea.xvg

What I don't understand is why there are 3 columns in the file 
resarea.xvg although this is what's written in my file:

# g_sas is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@title "Area per residue"
@xaxis  label "Residue"
@yaxis  label "Area (nm\S2\N)"
@TYPE xy

So I would expect this file to contain only two columns. I'm using 
gromacs version 4.0.3.




Residue, average area, standard deviation.

-Justin


Thanks for your help,
Carla



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] g_hbond

[Erik Marklund]

Hi,

Let me have a look at the files off-list and I'll probably see what's 
going on.


Erik

Carla Jamous skrev 2010-11-04 11.32:

Hi Erik,

I tried what you said: I made index groups containing only the atoms 
involved in that hbond and ran g_hbond again. The problem didn't persist.
So I wanted to check if I misinterpreted the map: for that, I compared 
my 4 index files: the one of my concatenated trajectory and the three 
of the separate trajectories.
When I look at this comparison table and then at my concatenated hbond 
map, the results don't match: for example, the Hbond that has the 
number 1 in my concatenated trajectory doesn't appear in my 
concatenated map (it means that in my map, next to y=1, nothing 
appears), however, this same H-bond (same number of atoms involved) 
exists in my first and my third trajectories' index files. So please 
could you explain how to interpret the map and if next to some y value 
in my map, nothing appears, is this value taken into account in my 
index file?


Thank you,
Carla

On Tue, Nov 2, 2010 at 8:36 PM, Erik Marklund > wrote:


Erik Marklund skrev 2010-11-02 20.33:

Carla Jamous skrev 2010-11-02 17.35:

Hi to all,

I'm sorry I'm asking again a question I asked a week ago
but I still haven't found my answer:

I concatenated 3 trajectories of 3 different molecules
(that have the same number of atoms) with trjcat: trjcat
-settime

Then I ran g_hbond on the concatenated trajectory, I got
an index.ndx file that contains an H-bond between the
Thr121 of my protein and an atom N2 of my ligand. This
H_bond  figures in the 3 trajectories when I look at the
hbmap of my concatenated trajectory.

On the other hand, I ran g_hbond on each of the 3
different trajectories. This H_bond doesn't exist in the
index files of two of my trajectories. So it doesn't match
the result I get with my concatenated trajectory.

To be sure that this result is right, I calculated the
angle and the r of my H-bond in VMD during each of the 3
trajectories and the results indicate that this H-bond
doesn't exist (I consider that r must be < or equal to
0.35 nm and angle < or equal to 30 degrees).

Please can anyone tell me why the results of g_hbond in my
concatenated trajectory don't match the results of g_hbond
on each of my trajectories?

Thank you

Carla

Hi,

This sounds strange. Could you file a bugzilla and either
upload the trajectories+tpr, or, if the files are huge, make
them available my other means? I need to have a closer look,
perhaps through a debugger.

A simple test you could do yourself is to make index groups
containing only the atoms involved in that hbond and run g_hbond
again. If the problem persists, then it looks like a bug. If not,
then I still can't rule out misinterpretation of the matrix.

Erik


-- 
---

Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.se 
http://folding.bmc.uu.se/

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--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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[gmx-users] tip3p itp file parameters

[Sai Pooja]

When using the charmm forcefield, the following is the case:

1. ffnonbonded.itp - has listed paramters for tip3p (and other water models)
OWT3  and HWT3
2. ffbonded.itp - does not have paramters for OWT3 and HWT3

Does this mean:

1. nonbonded parameters for tip3p are read from ffnonbonded.itp for ALL
nonbonded interactions OR
for water-water interactions are read from tip3p.itp file and for
protein-water are read from ffnonbonded.itp?

2.bonded paramters for tip3p are read from tip3p.itp file?

Pooja


-- 
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Re: [gmx-users] tip3p itp file parameters

[Justin A. Lemkul]

Sai Pooja wrote:

When using the charmm forcefield, the following is the case:
 
1. ffnonbonded.itp - has listed paramters for tip3p (and other water 
models) OWT3  and HWT3

2. ffbonded.itp - does not have paramters for OWT3 and HWT3
 
Does this mean:
 
1. nonbonded parameters for tip3p are read from ffnonbonded.itp for ALL 
nonbonded interactions OR
for water-water interactions are read from tip3p.itp file and for 
protein-water are read from ffnonbonded.itp?
 


Nonbonded interactions are applied uniformly, unless they are modified in a 
specific [nonbond_params] directive.  Isn't this something we've worked through 
before?


http://lists.gromacs.org/pipermail/gmx-users/2010-October/055332.html


2.bonded paramters for tip3p are read from tip3p.itp file?
 


Bonded parameters for water models are really only relevant if using a flexible 
model (which you shouldn't).  Otherwise, the SETTLE algorithm simply fixes the 
geometry.  This is all determined by the #ifdef FLEXIBLE statement in, for 
instance, tip3p.itp.


-Justin


Pooja


--
Quaerendo Invenietis-Seek and you shall discover.



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] box shape

[mustafa bilsel]

Dear Lina,
could you express these commands clearly? I am a new user!

editconf -f peptide.pdb/.gro -o peptide_center_in_simulation_
box.gro -center x/2 y/2 z/2 -box x y z
genbox   -cp peptide_center_in_simulation_box.gro -cs spc216.gro -o
they_are_in_the_same_box_now.gro -p topol.top
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[gmx-users] deform option

[Green]

Hi,

I posted this question earlier but no-one answered it to me so I am going to
ask this question again.
On deform option in .mdp file, what is being done if you are shearing the
system? i.e., if I do:

deform = 0 0 0 1 0 0

it seems to change box-xy value. but what does it mean?

thanks,

gc
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Re: [gmx-users] box shape

[Justin A. Lemkul]

mustafa bilsel wrote:

Dear Lina,
could you express these commands clearly? I am a new user!



You've been given commands that are almost exactly what you should enter in a 
terminal.  I would suggest you describe exactly why they aren't clear.



editconf -f peptide.pdb/.gro -o peptide_center_in_simulation_
box.gro -center x/2 y/2 z/2 -box x y z


The only comment I have here is that, for trivial centering within a box, 
neither -center nor -c is explicitly needed.  When defining a unit cell with 
either -box or -d, centering is implied.  Replace "x y z" with whatever box 
dimensions you want.


genbox   -cp peptide_center_in_simulation_box.gro -cs spc216.gro -o 
they_are_in_the_same_box_now.gro -p topol.top




This command can be used as is, replacing filenames as necessary.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] tip3p itp file parameters

[Sai Pooja]

Thanks Justin. I was just making sure that I was modifying the relevant
files.
On Thu, Nov 4, 2010 at 2:17 PM, Justin A. Lemkul  wrote:

>
>
> Sai Pooja wrote:
>
>> When using the charmm forcefield, the following is the case:
>>  1. ffnonbonded.itp - has listed paramters for tip3p (and other water
>> models) OWT3  and HWT3
>> 2. ffbonded.itp - does not have paramters for OWT3 and HWT3
>>  Does this mean:
>>  1. nonbonded parameters for tip3p are read from ffnonbonded.itp for ALL
>> nonbonded interactions OR
>> for water-water interactions are read from tip3p.itp file and for
>> protein-water are read from ffnonbonded.itp?
>>
>>
>
> Nonbonded interactions are applied uniformly, unless they are modified in a
> specific [nonbond_params] directive.  Isn't this something we've worked
> through before?
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-October/055332.html
>
>
> 2.bonded paramters for tip3p are read from tip3p.itp file?
>>
>>
>
> Bonded parameters for water models are really only relevant if using a
> flexible model (which you shouldn't).  Otherwise, the SETTLE algorithm
> simply fixes the geometry.  This is all determined by the #ifdef FLEXIBLE
> statement in, for instance, tip3p.itp.
>
> -Justin
>
>
> Pooja
>>
>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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] GB-polarization

[Per Larsson]

Hi!

Yes, the GB-polarization energy corresponds to the solvent-solute 
electrostatics polarization energy.
The non-polar part of the solvation energy (the solvent-solvent cavity term and 
the solute-solvent vdw-term) are named Non. polar solvation (or something like 
that) in the log-file.

/Per
 
4 nov 2010 kl. 11.10 skrev Christian Mücksch:

> Dear all,
> 
> I've got a general question regarding implicit solvent simulations.
> Using g_energy there's an option to print out the GB-polarization. Is that 
> the solvent-solute electrostatics polarization free energy?
> 
> How can one interpret a rise or decrease in the GB-polarization?
> 
> Kind regards,
> 
> -- 
> Christian Mücksch
> Department of Physics
> TU Kaiserslautern
> Erwin Schrödinger Straße
> 67663 Kaiserslautern
> Germany
> 
> Phone: +49 (0)631 205 4287
> Email: mueck...@rhrk.uni-kl.de
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Re: [gmx-users] tip3p itp file parameters

[Mark Abraham]

On 5/11/2010 6:36 AM, Sai Pooja wrote:
Thanks Justin. I was just making sure that I was modifying the 
relevant files.


You can verify things for yourself by making a .tpr, making the change, 
making the new .tpr and then using gmxcheck to compare the two.


Mark

On Thu, Nov 4, 2010 at 2:17 PM, Justin A. Lemkul > wrote:




Sai Pooja wrote:

When using the charmm forcefield, the following is the case:
 1. ffnonbonded.itp - has listed paramters for tip3p (and
other water models) OWT3  and HWT3
2. ffbonded.itp - does not have paramters for OWT3 and HWT3
 Does this mean:
 1. nonbonded parameters for tip3p are read from
ffnonbonded.itp for ALL nonbonded interactions OR
for water-water interactions are read from tip3p.itp file and
for protein-water are read from ffnonbonded.itp?


Nonbonded interactions are applied uniformly, unless they are
modified in a specific [nonbond_params] directive.  Isn't this
something we've worked through before?

http://lists.gromacs.org/pipermail/gmx-users/2010-October/055332.html


2.bonded paramters for tip3p are read from tip3p.itp file?


Bonded parameters for water models are really only relevant if
using a flexible model (which you shouldn't).  Otherwise, the
SETTLE algorithm simply fixes the geometry.  This is all
determined by the #ifdef FLEXIBLE statement in, for instance,
tip3p.itp.

-Justin


Pooja


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Quaerendo Invenietis-Seek and you shall discover.



-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Targeted Energy Minimization

[Yao Yao]

Hi Gmxers,
Is that possible that in mdp file, only a specifically-targeted part inside/of 
the protein is energy minimized (EM)? Like, just wanna EM the ligand or one out 
of the two proteins in protein-docking.
Thanks in advance,
Yao


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