[gmx-users] LIGAND TOPOLOGY

[MUSYOKA THOMMAS]

Dear users,
I have been trying to build la ligand topology of my ligand through the
PRODRG web server.
I have the following queries;
According to Justin's important tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html
i am lost on how to allocate equivalent charges to equivalent groups. I
have read the recommended paper but seems still i have issues in allocating
the correct charges to my groups.

Secondly, its about how to determine which groups are encompassed by a
charge group

Attached find in my PRODRG input file.
Someone out there help me in understanding this.
Thanks in advance.
--

*MUSYOKA THOMMAS MUTEMI
Mob nos **+27844846540**
B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science
(Nagasaki University)*
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*Skype ID- MUSYOKA THOMMAS MUTEMI
Alternative email - thom...@sia.co.ke
*

"Do all the good you can,
By all the means you can,
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At all the times you can,
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[gmx-users] Regarding coordinate mismatching.

[sanjay choubey]

Hi,
 I am running membrane dynamics. After giving this commnad 


> grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

  i am receiving the following errors: 
Generated 837 of the 2346 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...

---
Program grompp, VERSION 4.5.5
Source code file: grompp.c, line: 523

Fatal error:
number of coordinates in coordinate file (em.gro, 44494)
             does not match topology (topol.top, 43374)
 

                                                   I am not getting how to 
rectify the error, number of coordinates in coordinate file em.gro(44494) 
doesnot 
 match topology(topol.top, 43374).
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Re: [gmx-users] LIGAND TOPOLOGY

[Justin Lemkul]

On 8/27/13 5:10 AM, MUSYOKA THOMMAS wrote:

Dear users,
I have been trying to build la ligand topology of my ligand through the
PRODRG web server.
I have the following queries;
According to Justin's important tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html
i am lost on how to allocate equivalent charges to equivalent groups. I
have read the recommended paper but seems still i have issues in allocating
the correct charges to my groups.



You'll have to be a lot more specific with what you're dealing with and what 
you're doing if you want to get any useful help.



Secondly, its about how to determine which groups are encompassed by a
charge group

Attached find in my PRODRG input file.


Attachments are not allowed on the mailing list.


Someone out there help me in understanding this.


Charge groups are used in the Gromos96 force fields and typically contain 2-4 
atoms such that the group has an integral charge (generally -1, 0, or 1). 
Figures 1, 3, 4, and 5 of our paper (dx.doi.org/10.1021/ci100335w) show how to 
properly assign charge groups in molecules of increasing complexity.  Our work 
should have encompassed almost all of the most commonly encountered functional 
groups.  Other examples for well-known molecules can be found in the .rtp file 
for the force field.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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Re: [gmx-users] Regarding coordinate mismatching.

[Justin Lemkul]

On 8/27/13 5:59 AM, sanjay choubey wrote:

Hi,
  I am running membrane dynamics. After giving this commnad



grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr


   i am receiving the following errors:
Generated 837 of the 2346 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...

---
Program grompp, VERSION 4.5.5
Source code file: grompp.c, line: 523

Fatal error:
number of coordinates in coordinate file (em.gro, 44494)
  does not match topology (topol.top, 43374)
  

I am not getting how to 
rectify the error, number of coordinates in coordinate file em.gro(44494) 
doesnot
  match topology(topol.top, 43374).



The answer is always bookkeeping.  You haven't correctly accounted for some part 
of the system in the [molecules] directive.  The difference is 1120, so it's not 
related to water molecules.  You also say you're running a membrane system, but 
I see no evidence of lipids in the grompp output, but if indeed there are 
lipids, you likely had to remove some to accommodate the protein, but didn't 
remove them from the topology.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Re: GPU version of Gromacs

[grita]

Hi,

Is it possible to calc the PME on the CUDA card?

If it is possible, how can one do it?

Best,
grita



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[gmx-users] general question about molecule.rtp and pdb2gmx

[Valentina]

Hi, a general question about writing molecule.rtp and how pdb2gmx treats it.

I have a few atom types and a few atoms per each atom type.

So a question - when I define interactions, say [ bonds ] can I define them
by atomtype, rather that atom number?!

*So like this:*
[ B31 ] 
  [ atoms ]
; atomname atomtype charge chargegroup
   o1  oc15  -1.00   0
   h1  hoz0.30  0
   o2  oc18  -0.875   1
   h2  hoy0.350  1
   o3  oc21  -0.875   1
   h3  hoy0.350  1
   o4  oc17  -0.875   2
   h4  hoy0.350  2
   mg1 mg1.403
   al1 ac31.35   4
   o5  oc16  -0.875   5
   h5  hoy0.350  5
   o6  oc20  -0.875   2
   h6  hoy0.350  2
   o7  oc19  -0.875   5
   h7  hoy0.350  5
   o8  oc15   -1.006
   h8  hoz0.30  6
   mg2 mg   1.40   7
   mg3 mg   1.40   8
  [ bonds ]
 ; atom1 atom2   parametersindex
   oc15 hoz b_oc-h
   oc16 hoy b_oc-h
   oc17 hoy b_oc-h
   oc18 hoy b_oc-h
   oc19 hoy b_oc-h
   oc20 hoy b_oc-h
   oc21 hoy b_oc-h
  ac3   oc16a_oc-ac-h
  ac3   oc17a_oc-ac-h
  ac3   oc18a_oc-ac-h
  ac3   oc19a_oc-ac-h
  ac3   oc20a_oc-ac-h
  ac3   oc21a_oc-ac-h

*Rather than like this:*
[ B31 ] ;
  [ atoms ]
; atomname atomtype charge chargegroup
   o1  oc15  -1.00   0
   h1  hoz0.30  0
   o2  oc18  -0.875   1
   h2  hoy0.350  1
   o3  oc21  -0.875   1
   h3  hoy0.350  1
   o4  oc17  -0.875   2
   h4  hoy0.350  2
   mg1 mg1.403
   al1 ac31.35   4
   o5  oc16  -0.875   5
   h5  hoy0.350  5
   o6  oc20  -0.875   2
   h6  hoy0.350  2
   o7  oc19  -0.875   5
   h7  hoy0.350  5
   o8  oc15   -1.006
   h8  hoz0.30  6
   mg2 mg   1.40   7
   mg3 mg   1.40   8
  [ bonds ]
 ; atom1 atom2   parametersindex
   o1 h1 b_oc-h
   o2 h2 b_oc-h
   o3 h3 b_oc-h
   o4 h4 b_oc-h
   o5 h5 b_oc-h
   o6 h6 b_oc-h
   o7 h7 b_oc-h
   o8 h8 b_oc-h
   al1  o5  a_oc-ac-h
   al1  o4  a_oc-ac-h
   al1  o2  a_oc-ac-h
   al1  o7  a_oc-ac-h
   al1  o6  a_oc-ac-h
   al1  o3  a_oc-ac-h


If I use the 1st I get .top that does not list interactions, just [ atoms ]
and #include link to the FF. Is this still OK? Does it read the [ bonds ]
interactions or just non bonded?

Thank you,
V





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Re: [gmx-users] Re: GPU version of Gromacs

[Mark Abraham]

No, that is not implemented. Roughly speaking, the CPU does the
PME+bondeds while the GPU does the short-ranged interactions. Moving
PME would only be worthwhile if there was a very weak CPU and it was
cheap to do any necessary communication between GPUs. That day is not
yet here :-)

Mark

On Tue, Aug 27, 2013 at 4:17 PM, grita  wrote:
> Hi,
>
> Is it possible to calc the PME on the CUDA card?
>
> If it is possible, how can one do it?
>
> Best,
> grita
>
>
>
> --
> View this message in context: 
> http://gromacs.5086.x6.nabble.com/GPU-version-of-Gromacs-tp5010581p5010758.html
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Re: [gmx-users] general question about molecule.rtp and pdb2gmx

[Justin Lemkul]

On 8/27/13 12:30 PM, Valentina wrote:

Hi, a general question about writing molecule.rtp and how pdb2gmx treats it.

I have a few atom types and a few atoms per each atom type.

So a question - when I define interactions, say [ bonds ] can I define them
by atomtype, rather that atom number?!

*So like this:*
[ B31 ]
   [ atoms ]
; atomname atomtype charge chargegroup
o1  oc15  -1.00   0
h1  hoz0.30  0
o2  oc18  -0.875   1
h2  hoy0.350  1
o3  oc21  -0.875   1
h3  hoy0.350  1
o4  oc17  -0.875   2
h4  hoy0.350  2
mg1 mg1.403
al1 ac31.35   4
o5  oc16  -0.875   5
h5  hoy0.350  5
o6  oc20  -0.875   2
h6  hoy0.350  2
o7  oc19  -0.875   5
h7  hoy0.350  5
o8  oc15   -1.006
h8  hoz0.30  6
mg2 mg   1.40   7
mg3 mg   1.40   8
   [ bonds ]
  ; atom1 atom2   parametersindex
oc15 hoz b_oc-h
oc16 hoy b_oc-h
oc17 hoy b_oc-h
oc18 hoy b_oc-h
oc19 hoy b_oc-h
oc20 hoy b_oc-h
oc21 hoy b_oc-h
   ac3  oc16a_oc-ac-h
   ac3  oc17a_oc-ac-h
   ac3  oc18a_oc-ac-h
   ac3  oc19a_oc-ac-h
   ac3  oc20a_oc-ac-h
   ac3  oc21a_oc-ac-h

*Rather than like this:*
[ B31 ] ;
   [ atoms ]
; atomname atomtype charge chargegroup
o1  oc15  -1.00   0
h1  hoz0.30  0
o2  oc18  -0.875   1
h2  hoy0.350  1
o3  oc21  -0.875   1
h3  hoy0.350  1
o4  oc17  -0.875   2
h4  hoy0.350  2
mg1 mg1.403
al1 ac31.35   4
o5  oc16  -0.875   5
h5  hoy0.350  5
o6  oc20  -0.875   2
h6  hoy0.350  2
o7  oc19  -0.875   5
h7  hoy0.350  5
o8  oc15   -1.006
h8  hoz0.30  6
mg2 mg   1.40   7
mg3 mg   1.40   8
   [ bonds ]
  ; atom1 atom2   parametersindex
o1 h1 b_oc-h
o2 h2 b_oc-h
o3 h3 b_oc-h
o4 h4 b_oc-h
o5 h5 b_oc-h
o6 h6 b_oc-h
o7 h7 b_oc-h
o8 h8 b_oc-h
al1 o5  a_oc-ac-h
al1 o4  a_oc-ac-h
al1 o2  a_oc-ac-h
al1 o7  a_oc-ac-h
al1 o6  a_oc-ac-h
al1 o3  a_oc-ac-h



Defining by type is ambiguous.  An .rtp requires that atom names be used to 
define connectivity.




If I use the 1st I get .top that does not list interactions, just [ atoms ]
and #include link to the FF. Is this still OK? Does it read the [ bonds ]
interactions or just non bonded?



No, it's not OK.  In that case, you have no bonds at all, so your molecule would 
go flying apart.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] general question about molecule.rtp and pdb2gmx

[Mark Abraham]

.rtp [bonds] requires atom names (because that's all that can be
reliably deduced from the coordinate file input)
.itp/.top [bonds] requires atom numbers (because prior sanity-ization
is assumed) to look up the atom types to look up the interaction
parameters

... and different force fields have slightly different details. Ain't life fun?

Mark

On Tue, Aug 27, 2013 at 6:33 PM, Justin Lemkul  wrote:
>
>
> On 8/27/13 12:30 PM, Valentina wrote:
>>
>> Hi, a general question about writing molecule.rtp and how pdb2gmx treats
>> it.
>>
>> I have a few atom types and a few atoms per each atom type.
>>
>> So a question - when I define interactions, say [ bonds ] can I define
>> them
>> by atomtype, rather that atom number?!
>>
>> *So like this:*
>> [ B31 ]
>>[ atoms ]
>> ; atomname atomtype charge chargegroup
>> o1  oc15  -1.00   0
>> h1  hoz0.30  0
>> o2  oc18  -0.875   1
>> h2  hoy0.350  1
>> o3  oc21  -0.875   1
>> h3  hoy0.350  1
>> o4  oc17  -0.875   2
>> h4  hoy0.350  2
>> mg1 mg1.403
>> al1 ac31.35   4
>> o5  oc16  -0.875   5
>> h5  hoy0.350  5
>> o6  oc20  -0.875   2
>> h6  hoy0.350  2
>> o7  oc19  -0.875   5
>> h7  hoy0.350  5
>> o8  oc15   -1.006
>> h8  hoz0.30  6
>> mg2 mg   1.40   7
>> mg3 mg   1.40   8
>>[ bonds ]
>>   ; atom1 atom2   parametersindex
>> oc15 hoz b_oc-h
>> oc16 hoy b_oc-h
>> oc17 hoy b_oc-h
>> oc18 hoy b_oc-h
>> oc19 hoy b_oc-h
>> oc20 hoy b_oc-h
>> oc21 hoy b_oc-h
>>ac3  oc16a_oc-ac-h
>>ac3  oc17a_oc-ac-h
>>ac3  oc18a_oc-ac-h
>>ac3  oc19a_oc-ac-h
>>ac3  oc20a_oc-ac-h
>>ac3  oc21a_oc-ac-h
>>
>> *Rather than like this:*
>> [ B31 ] ;
>>[ atoms ]
>> ; atomname atomtype charge chargegroup
>> o1  oc15  -1.00   0
>> h1  hoz0.30  0
>> o2  oc18  -0.875   1
>> h2  hoy0.350  1
>> o3  oc21  -0.875   1
>> h3  hoy0.350  1
>> o4  oc17  -0.875   2
>> h4  hoy0.350  2
>> mg1 mg1.403
>> al1 ac31.35   4
>> o5  oc16  -0.875   5
>> h5  hoy0.350  5
>> o6  oc20  -0.875   2
>> h6  hoy0.350  2
>> o7  oc19  -0.875   5
>> h7  hoy0.350  5
>> o8  oc15   -1.006
>> h8  hoz0.30  6
>> mg2 mg   1.40   7
>> mg3 mg   1.40   8
>>[ bonds ]
>>   ; atom1 atom2   parametersindex
>> o1 h1 b_oc-h
>> o2 h2 b_oc-h
>> o3 h3 b_oc-h
>> o4 h4 b_oc-h
>> o5 h5 b_oc-h
>> o6 h6 b_oc-h
>> o7 h7 b_oc-h
>> o8 h8 b_oc-h
>> al1 o5  a_oc-ac-h
>> al1 o4  a_oc-ac-h
>> al1 o2  a_oc-ac-h
>> al1 o7  a_oc-ac-h
>> al1 o6  a_oc-ac-h
>> al1 o3  a_oc-ac-h
>>
>
> Defining by type is ambiguous.  An .rtp requires that atom names be used to
> define connectivity.
>
>
>>
>> If I use the 1st I get .top that does not list interactions, just [ atoms
>> ]
>> and #include link to the FF. Is this still OK? Does it read the [ bonds ]
>> interactions or just non bonded?
>>
>
> No, it's not OK.  In that case, you have no bonds at all, so your molecule
> would go flying apart.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
>
> --
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[gmx-users] Re: general question about molecule.rtp and pdb2gmx

[Valentina]

Ok, thank you!

I was hoping for an easier job.

My system is anyhow flying apart - trying to spot a problem. Hence trying.

One more question - [ pairs ] get automatically generated. But I don't need
1-4 LJ. So I can just remove them?

Thank you



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[gmx-users] About script for free energy calculation

[vidhya sankar]

Dear Justin thank you for your Previous reply
  I am following your methane/water free energy tutorial
I have Generated All .mdp files wiht Different LAMBDA value But When I Run job 
using Your Job.sh  script
 in usr/local/gromacs4.6.2/bin I have Received the Following error  ( I ma 
running this script by keepig in BIN directory)

root@vidhyasankar-desktop:/usr/local/gromacs4.6.1/bin# ./job.sh  ( the error is 
as follows)


Free energy home directory set to /usr/local/gromacs4.6.1/bin/Free_Energy
.mdp files are stored in /usr/local/gromacs4.6.1/bin/Free_Energy/MDP
Starting minimization for lambda = 0...
./job.sh: line 28: grompp_d: command not found
./job.sh: line 30: mdrun_d: command not found
./job.sh: line 41: grompp_d: command not found
./job.sh: line 45: mdrun_d: command not found
Minimization complete.
Starting constant volume equilibration...
./job.sh: line 60: grompp_d: command not found
./job.sh: line 62: mdrun_d: command not found
Constant volume equilibration complete.
Starting constant pressure equilibration...
./job.sh: line 77: grompp_d: command not found
./job.sh: line 79: mdrun_d: command not found
Constant pressure equilibration complete.
Starting production MD simulation...
./job.sh: line 93: grompp_d: command not found
./job.sh: line 95: mdrun_d: command not found
Production MD complete.
Ending. Job completed for lambda = 0

How to Solve it 

Thanks InAdvance

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Re: [gmx-users] About script for free energy calculation

[Mark Abraham]

On Tue, Aug 27, 2013 at 7:05 PM, vidhya sankar  wrote:
> Dear Justin thank you for your Previous reply
>   I am following your methane/water free energy tutorial
> I have Generated All .mdp files wiht Different LAMBDA value But When I Run 
> job using Your Job.sh  script
>  in usr/local/gromacs4.6.2/bin I have Received the Following error  ( I ma 
> running this script by keepig in BIN directory)

Don't. Your root privileges have just been revoked. :-) Learn to
source GMXRC like the installation instructions say.

Mark

> root@vidhyasankar-desktop:/usr/local/gromacs4.6.1/bin# ./job.sh  ( the error 
> is as follows)
>
>
> Free energy home directory set to /usr/local/gromacs4.6.1/bin/Free_Energy
> .mdp files are stored in /usr/local/gromacs4.6.1/bin/Free_Energy/MDP
> Starting minimization for lambda = 0...
> ./job.sh: line 28: grompp_d: command not found
> ./job.sh: line 30: mdrun_d: command not found
> ./job.sh: line 41: grompp_d: command not found
> ./job.sh: line 45: mdrun_d: command not found
> Minimization complete.
> Starting constant volume equilibration...
> ./job.sh: line 60: grompp_d: command not found
> ./job.sh: line 62: mdrun_d: command not found
> Constant volume equilibration complete.
> Starting constant pressure equilibration...
> ./job.sh: line 77: grompp_d: command not found
> ./job.sh: line 79: mdrun_d: command not found
> Constant pressure equilibration complete.
> Starting production MD simulation...
> ./job.sh: line 93: grompp_d: command not found
> ./job.sh: line 95: mdrun_d: command not found
> Production MD complete.
> Ending. Job completed for lambda = 0
>
> How to Solve it
>
> Thanks InAdvance
>
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Re: [gmx-users] Re: general question about molecule.rtp and pdb2gmx

[Sergey]

Yes, can remove.
However, ability to remove don't depend on our desire,
but depend on Force field set of rules. If molecule
was parametrized with 1-4 LJ, it is not desirable to remove it.

If it is in-house force field which  ignore 1-4 LJ, then one can
safely remove it.

Sergey


27.08.2013, 20:42, "Valentina" :
> Ok, thank you!
>
> I was hoping for an easier job.
>
> My system is anyhow flying apart - trying to spot a problem. Hence trying.
>
> One more question - [ pairs ] get automatically generated. But I don't need
> 1-4 LJ. So I can just remove them?
>
> Thank you
>
> --
> View this message in context: 
> http://gromacs.5086.x6.nabble.com/general-question-about-molecule-rtp-and-pdb2gmx-tp5010759p5010761.html
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[gmx-users] Re: general question about molecule.rtp and pdb2gmx

[Valentina]

Yes - own parameters. Just thought gen-pairs in [ defaults ] should prevent
this output.
Thank you



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Re: [gmx-users] Help with Error Message

[Tsjerk Wassenaar]

Hey :)

Sorry for replying a bit late. But the issues you mention in this and the
other posts are usually solved by closely reading the text of the tutorial,
not only the commands.

Cheers,

Tsjerk


On Sun, Aug 25, 2013 at 3:44 AM, The One And Only wrote:

> Never mind, I'm dumb. I just realized that protein.pdb means i have to
> specify which protein i want like "1qlz.pdb" and not actually type
> "protein.pdb" BUT THANKS GUYS!!
>
>
> On Sat, Aug 24, 2013 at 6:40 PM, The One And Only  >wrote:
>
> > so how do i solve the protein.pdb issue?
> >
> >
> > On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 8/24/13 9:26 PM, The One And Only wrote:
> >>
> >>> that's something i know nothing about; I just graduated from high
> school
> >>> and I have no background or experience in open source projects or
> >>> programs
> >>> like pymol/gromacs. My professor wants me to be able to produce a
> setup,
> >>> simulation, and analysis within a week so I'm pretty desperate right
> now
> >>> in
> >>> terms of getting help. Do you know how to get the right .pdb file in my
> >>> working directory?
> >>>
> >>>
> >> Rudimentary Unix commands like cp and mv are covered in any Unix/Linux
> >> tutorial.  Google can find lots of good ones.  Producing a quality
> >> simulation cannot be rushed, and if you don't know the fundamentals of
> >> navigating the command line and directory structure, it's nearly
> >> impossible.  You need to invest time in learning the environment before
> >> doing anything, I'm afraid.  Just to give a bit of perspective, we used
> to
> >> train our undergrads for nearly a full semester (at least 2-3 months)
> >> before requiring them to do any "real" work.  At least a week or two of
> >> that time was spent getting used to command line and Linux in general.
> >>
> >> -Justin
> >>
> >> --
> >> ==**
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 601
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul@outerbanks.umaryland.**edu |
> (410)
> >> 706-7441
> >>
> >> ==**
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> >> * Please search the archive at http://www.gromacs.org/**
> >> Support/Mailing_Lists/Search<
> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
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> >> interface or send it to gmx-users-requ...@gromacs.org.
> >> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> http://www.gromacs.org/Support/Mailing_Lists>
> >>
> >
> >
> --
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-- 
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Re: [gmx-users] Re: general question about molecule.rtp and pdb2gmx

[Justin Lemkul]

On 8/27/13 4:25 PM, Valentina wrote:

Yes - own parameters. Just thought gen-pairs in [ defaults ] should prevent
this output.


No, that's not how gen-pairs works.  There are many excellent explanations of 
how it works in the list archive, but suffice it to say it does not affect the 
appearance of pairs, instead it affects what parameters are applied (either 
looked up or generated).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Help with Error Message

[The One And Only]

I've moved on from that point; now I'm stuck at where it asks me to remove
molecules of solvent from the topology file.


On Tue, Aug 27, 2013 at 1:33 PM, Tsjerk Wassenaar  wrote:

> Hey :)
>
> Sorry for replying a bit late. But the issues you mention in this and the
> other posts are usually solved by closely reading the text of the tutorial,
> not only the commands.
>
> Cheers,
>
> Tsjerk
>
>
> On Sun, Aug 25, 2013 at 3:44 AM, The One And Only  >wrote:
>
> > Never mind, I'm dumb. I just realized that protein.pdb means i have to
> > specify which protein i want like "1qlz.pdb" and not actually type
> > "protein.pdb" BUT THANKS GUYS!!
> >
> >
> > On Sat, Aug 24, 2013 at 6:40 PM, The One And Only  > >wrote:
> >
> > > so how do i solve the protein.pdb issue?
> > >
> > >
> > > On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul 
> wrote:
> > >
> > >>
> > >>
> > >> On 8/24/13 9:26 PM, The One And Only wrote:
> > >>
> > >>> that's something i know nothing about; I just graduated from high
> > school
> > >>> and I have no background or experience in open source projects or
> > >>> programs
> > >>> like pymol/gromacs. My professor wants me to be able to produce a
> > setup,
> > >>> simulation, and analysis within a week so I'm pretty desperate right
> > now
> > >>> in
> > >>> terms of getting help. Do you know how to get the right .pdb file in
> my
> > >>> working directory?
> > >>>
> > >>>
> > >> Rudimentary Unix commands like cp and mv are covered in any Unix/Linux
> > >> tutorial.  Google can find lots of good ones.  Producing a quality
> > >> simulation cannot be rushed, and if you don't know the fundamentals of
> > >> navigating the command line and directory structure, it's nearly
> > >> impossible.  You need to invest time in learning the environment
> before
> > >> doing anything, I'm afraid.  Just to give a bit of perspective, we
> used
> > to
> > >> train our undergrads for nearly a full semester (at least 2-3 months)
> > >> before requiring them to do any "real" work.  At least a week or two
> of
> > >> that time was spent getting used to command line and Linux in general.
> > >>
> > >> -Justin
> > >>
> > >> --
> > >> ==**
> > >>
> > >> Justin A. Lemkul, Ph.D.
> > >> Postdoctoral Fellow
> > >>
> > >> Department of Pharmaceutical Sciences
> > >> School of Pharmacy
> > >> Health Sciences Facility II, Room 601
> > >> University of Maryland, Baltimore
> > >> 20 Penn St.
> > >> Baltimore, MD 21201
> > >>
> > >> jalemkul@outerbanks.umaryland.**edu <
> jalem...@outerbanks.umaryland.edu>|
> > (410)
> > >> 706-7441
> > >>
> > >> ==**
> > >> --
> > >> gmx-users mailing listgmx-users@gromacs.org
> > >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > >> * Please search the archive at http://www.gromacs.org/**
> > >> Support/Mailing_Lists/Search<
> > 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<
> > http://www.gromacs.org/Support/Mailing_Lists>
> > >>
> > >
> > >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
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> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Help with Error Message

[Tsjerk Wassenaar]

Hi ...,

You should have had a look at the topology file format in an earlier step.
At the end is a listing of molecules. As it says in the tutorial, you
replaced solvent by ions, and you have to make changes in the topology file
to match that replacement. Open the file in an editor, have a look around,
try to see where the number of solvent molecules is listed, and make the
changes.

Cheers,

Tsjerk


On Tue, Aug 27, 2013 at 10:41 PM, The One And Only wrote:

> I've moved on from that point; now I'm stuck at where it asks me to remove
> molecules of solvent from the topology file.
>
>
> On Tue, Aug 27, 2013 at 1:33 PM, Tsjerk Wassenaar 
> wrote:
>
> > Hey :)
> >
> > Sorry for replying a bit late. But the issues you mention in this and the
> > other posts are usually solved by closely reading the text of the
> tutorial,
> > not only the commands.
> >
> > Cheers,
> >
> > Tsjerk
> >
> >
> > On Sun, Aug 25, 2013 at 3:44 AM, The One And Only  > >wrote:
> >
> > > Never mind, I'm dumb. I just realized that protein.pdb means i have to
> > > specify which protein i want like "1qlz.pdb" and not actually type
> > > "protein.pdb" BUT THANKS GUYS!!
> > >
> > >
> > > On Sat, Aug 24, 2013 at 6:40 PM, The One And Only <
> chappybo...@gmail.com
> > > >wrote:
> > >
> > > > so how do i solve the protein.pdb issue?
> > > >
> > > >
> > > > On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul 
> > wrote:
> > > >
> > > >>
> > > >>
> > > >> On 8/24/13 9:26 PM, The One And Only wrote:
> > > >>
> > > >>> that's something i know nothing about; I just graduated from high
> > > school
> > > >>> and I have no background or experience in open source projects or
> > > >>> programs
> > > >>> like pymol/gromacs. My professor wants me to be able to produce a
> > > setup,
> > > >>> simulation, and analysis within a week so I'm pretty desperate
> right
> > > now
> > > >>> in
> > > >>> terms of getting help. Do you know how to get the right .pdb file
> in
> > my
> > > >>> working directory?
> > > >>>
> > > >>>
> > > >> Rudimentary Unix commands like cp and mv are covered in any
> Unix/Linux
> > > >> tutorial.  Google can find lots of good ones.  Producing a quality
> > > >> simulation cannot be rushed, and if you don't know the fundamentals
> of
> > > >> navigating the command line and directory structure, it's nearly
> > > >> impossible.  You need to invest time in learning the environment
> > before
> > > >> doing anything, I'm afraid.  Just to give a bit of perspective, we
> > used
> > > to
> > > >> train our undergrads for nearly a full semester (at least 2-3
> months)
> > > >> before requiring them to do any "real" work.  At least a week or two
> > of
> > > >> that time was spent getting used to command line and Linux in
> general.
> > > >>
> > > >> -Justin
> > > >>
> > > >> --
> > > >> ==**
> > > >>
> > > >> Justin A. Lemkul, Ph.D.
> > > >> Postdoctoral Fellow
> > > >>
> > > >> Department of Pharmaceutical Sciences
> > > >> School of Pharmacy
> > > >> Health Sciences Facility II, Room 601
> > > >> University of Maryland, Baltimore
> > > >> 20 Penn St.
> > > >> Baltimore, MD 21201
> > > >>
> > > >> jalemkul@outerbanks.umaryland.**edu <
> > jalem...@outerbanks.umaryland.edu>|
> > > (410)
> > > >> 706-7441
> > > >>
> > > >> ==**
> > > >> --
> > > >> gmx-users mailing listgmx-users@gromacs.org
> > > >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > > >> * Please search the archive at http://www.gromacs.org/**
> > > >> Support/Mailing_Lists/Search<
> > > 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<
> > > http://www.gromacs.org/Support/Mailing_Lists>
> > > >>
> > > >
> > > >
> > > --
> > > 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!
> > > * 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
> > >
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
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> >
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.g

Re: [gmx-users] Help with Error Message

[The One And Only]

What kind of editor should I open it in? I have Pymol, but I don't know if
it's the right one.
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Re: [gmx-users] Help with Error Message

[Rafael I. Silverman y de la Vega]

a text editor


On Tue, Aug 27, 2013 at 1:54 PM, The One And Only wrote:

> What kind of editor should I open it in? I have Pymol, but I don't know if
> it's the right one.
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Help with Error Message

[Tsjerk Wassenaar]

An editor is a program to edit the text in a file: gedit, nano, vi, emacs,
... It'll be the equivalent of Windows' Notepad. Can you find a tutor
around to help you out with the basic usage of Linux? It's always difficult
to plunge into several different things at the same time, here 'using
linux', 'performing simulations', and probably 'theory of molecular
dynamics'. It helps to take one topic at a time, but that is not always
possible.

Cheers,

T.




On Tue, Aug 27, 2013 at 10:56 PM, Rafael I. Silverman y de la Vega <
rsilv...@ucsc.edu> wrote:

> a text editor
>
>
> On Tue, Aug 27, 2013 at 1:54 PM, The One And Only  >wrote:
>
> > What kind of editor should I open it in? I have Pymol, but I don't know
> if
> > it's the right one.
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
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[gmx-users] Rescale: Cloud simulation platform research grants

[Ilea Graedel]

My name is Ilea Graedel, and I work at Rescale (www.rescale.com), a
software company based in San Francisco, CA. Rescale provides a secure,
web-based platform for engineers, scientists, and researchers to perform
compute-intensive analyses in the cloud. We enable companies and academic
institutions to run simulations faster then they can today.

I'm writing to let you know that we have launched our first-ever Simulation
Research Grant competition as part of the Rescale University Program
(ReUP). Competition details are available
here as
well as below.  With these grants, select researchers will have the
opportunity to run their computing analyses and simulations for free on
Rescale’s platform.

Simulation Grant competition details:
http://www.rescale.com/reup/reup-grants.pdf

Feel free to email me (i...@rescale.com) if you have any questions.

Regards,
Ilea

-- 
*Ilea Graedel*
Manager, Business Development
Rescale
i...@rescale.com
+1 509 721 0629


This email is confidential and may be privileged. If you have received it
in error, please notify us immediately and then delete it.  Please do not
copy it, disclose its contents or use it for any purpose.

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[gmx-users] Wrapping of protein molecules during simulation

[Gianluca Interlandi]

Hi!

I noticed that gromacs breaks molecules due to PBC during the output of 
trajectories. I understand that this can be fixed with trjconv. Is there 
any option in the parameter file to force gromacs to keep molecules whole? 
If not is it for efficiency purposes?


Sorry, if this question might have been asked many times already, but I 
could not find an answer.


Thanks,

 Gianluca

-
Gianluca Interlandi, PhD gianl...@u.washington.edu
http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
http://healthynaturalbaby.org
-
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Re: [gmx-users] Wrapping of protein molecules during simulation

[Justin Lemkul]

On 8/27/13 8:02 PM, Gianluca Interlandi wrote:

Hi!

I noticed that gromacs breaks molecules due to PBC during the output of
trajectories. I understand that this can be fixed with trjconv. Is there any
option in the parameter file to force gromacs to keep molecules whole? If not is
it for efficiency purposes?



Doing so serves no functional purpose, so there is no reason mdrun should waste 
time reconstructing molecules during the run (obtaining atomic positions from 
domains, reconstructing from the topology, etc).  Many analysis tools don't even 
require "whole" molecules anyway; it's primarily a visualization convenience.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Gentle heating with implicit solvent

[Gianluca Interlandi]

How important is it to do gentle heating (using simulated annealing) with 
GBSA? Often with explicit water it is enough to perform some equilibration 
with positional restraints. Would it be enough to do the same with 
implicit solvent?


Thanks,

 Gianluca

-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
http://healthynaturalbaby.org
-
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[gmx-users] Genion command not working

[Deepak Ojha]

Dear Gmxers,

I want to simulate 5M nabr aqueous solution.To add the ions I use genion
command and add 22 na and br ions
respectively to the system of pure 108 water molecules.But on running the
command genion I get error message


Processing topology

Back Off! I just backed up topol.top to ./#topol.top.9#
Replacing solvent molecule 12 (atom 36) with NA
Replacing solvent molecule 52 (atom 156) with CL
Replacing solvent molecule 35 (atom 105) with NA
Replacing solvent molecule 17 (atom 51) with CL
Replacing solvent molecule 41 (atom 123) with NA
Replacing solvent molecule 70 (atom 210) with CL
Replacing solvent molecule 44 (atom 132) with NA
Replacing solvent molecule 66 (atom 198) with CL
Replacing solvent molecule 34 (atom 102) with NA
Replacing solvent molecule 29 (atom 87) with CL

---
Program genion, VERSION 4.0.7
Source code file: ../../../../src/tools/gmx_genion.c, line: 85

Fatal error:
No more replaceable solvent!
---




How should I add ions in the system.I have tried doing it but could not get
it please if someone may
point my error.


-- 
DeepaK Ojha
School Of Chemistry

"Selfishness is not living as one wishes to live, it is asking others to
live as one wishes to live"
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Re: [gmx-users] Genion command not working

[Tsjerk Wassenaar]

Hi Deepak,

You have to set the minimal distance between ions lower. Check the help of
genion.

Cheers,

Tsjerk

On Aug 28, 2013 8:04 AM, "Deepak Ojha"  wrote:

Dear Gmxers,

I want to simulate 5M nabr aqueous solution.To add the ions I use genion
command and add 22 na and br ions
respectively to the system of pure 108 water molecules.But on running the
command genion I get error message


Processing topology

Back Off! I just backed up topol.top to ./#topol.top.9#
Replacing solvent molecule 12 (atom 36) with NA
Replacing solvent molecule 52 (atom 156) with CL
Replacing solvent molecule 35 (atom 105) with NA
Replacing solvent molecule 17 (atom 51) with CL
Replacing solvent molecule 41 (atom 123) with NA
Replacing solvent molecule 70 (atom 210) with CL
Replacing solvent molecule 44 (atom 132) with NA
Replacing solvent molecule 66 (atom 198) with CL
Replacing solvent molecule 34 (atom 102) with NA
Replacing solvent molecule 29 (atom 87) with CL

---
Program genion, VERSION 4.0.7
Source code file: ../../../../src/tools/gmx_genion.c, line: 85

Fatal error:
No more replaceable solvent!
---




How should I add ions in the system.I have tried doing it but could not get
it please if someone may
point my error.


--
DeepaK Ojha
School Of Chemistry

"Selfishness is not living as one wishes to live, it is asking others to
live as one wishes to live"
--
gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] Long range Lennard Jones

[Gianluca Interlandi]

Hi!

Just wondering whether gromacs has (or plans to implement) a correction 
for the loss of long range LJ interactons? Something similar to 
LJcorrection in NAMD or IPS in CHARMM.


Thanks!

 Gianluca

-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
http://healthynaturalbaby.org
-
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RE: [gmx-users] Long range Lennard Jones

[Dallas Warren]

DispCorr might be what you are looking for, correction for LJ beyond the 
cut-off.

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 


> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Gianluca Interlandi
> Sent: Wednesday, 28 August 2013 4:36 PM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Long range Lennard Jones
> 
> Hi!
> 
> Just wondering whether gromacs has (or plans to implement) a correction
> for the loss of long range LJ interactons? Something similar to
> LJcorrection in NAMD or IPS in CHARMM.
> 
> Thanks!
> 
>   Gianluca
> 
> -
> Gianluca Interlandi, PhD gianl...@u.washington.edu
>  +1 (206) 685 4435
>  http://artemide.bioeng.washington.edu/
> 
> Research Scientist at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
>  http://healthynaturalbaby.org
> -
> --
> gmx-users mailing listgmx-users@gromacs.org
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