[gmx-users] simulating dimer proteins

[Justin A. Lemkul]

On 6/16/12 6:29 AM, delara aghaie wrote:
> Dear Mark
> Again some questions:
> ------------------------------------------
> I used -chainsep option to pdb2gmx and generated topology files for two protein
> chains and also .gro file containing both chains
> ........................................
> The energy minimization was done successfully and I got average pot.
> energy=-1.2*10^6
> Then I started NVT simulation for 200 ps with position restraints on proteins.
>
> 1)) having the following line in .mdp file will do position restraints on both
> chains, considering that each chan has its own .top file????

Yes, it does.  Position restraints are applied per [moleculetype], as indicated 
in the topology.

> define          = -DPOSRES      ; position restrain the protein
> ---------------------------------
> 200 ps, NVT simulation finished, but I think there is something wrong here. This
> is part of my nvt.mdp file:
>
> ; Temperature coupling is on
> tcoupl          = V-rescale     ; modified Berendsen thermostat
> tc-grps         = Protein Non-Protein   ; two coupling groups - more accurate
> tau_t           = 0.1   0.1     ; time constant, in ps
> ref_t           = 310   310     ; reference temperature, one for each group, in K
>
> As here my protein has two chains, is it necessary to increase the tc-groups???

No.  See the following:

http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do

-Justin

> I mean should I use for example
> tc-grps = Protein_chain_A Protein_chain_B SOl NA     (These are the names that
> are present at the end of topol.top file)
>
> Thanks
> Regards
> D.M
>
>
> --------------------------------------------------------------------------------
>
>
>
> --------------------------------------------------------------------------------
>
>
> *From:* Mark Abraham <Mark.Abraham at anu.edu.au>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Saturday, 16 June 2012, 12:15
> *Subject:* Re: [gmx-users] simulating dimer proteins
>
> On 16/06/2012 5:31 PM, delara aghaie wrote:
>> Dear Gromacs Users
>>
>> Running pdb2gmx on a pdb file containing a dimer protein, I used option ((
>> chainsep id_or_ter)))
>> This resulted in separated topologies for each chain and separated posre
>> files. Also in the .gro file, the aminoacides of the second chain started from
>> number 1. (Without this option the second chain aminoacides will receive
>> numbers in continuation of numbers of first chain))....
>>
>> Now:
>> Can I use these files to continue the simulations or again it is necessary to
>> follow the procedure explained in multiple chains gromacs???
>>
>
> By definition of pdb2gmx function, you now have a topology and a coordinate file
> that matches. That is the minimum requirement for grompp to succeed later.
> grompp doesn't care about some aspects of atom numbering - including your
> observation above.
>
> Mark
>
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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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