[gmx-users] numbering of .gro file

[Justin A. Lemkul]

Anna Marabotti wrote:
> Dear Mark,
> thank you also for your suggestion, indeed using the nvt.gro file with the
> sequential numbering I was able to distinguish the contributions from both
> chains, instead of seeing them superimposed.
> Now I have another question. I used pdb2gmx to prepare another file for
> simulation (it is the same protein as above, with a mutation). The pdb file
> contains two identical chains numbered starting from 21 to 379, marked with
> chain ID A and B.
> Using the command line:
> pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top
> I obtained a .gro file in which the numbering correctly starts from 21 to
> 379 in both chains, but no chain ID is present. I also tried to use
> -chainsep, but nothing changed. So my (last) question is: is there any way
> to avoid renumbering the file, but without obtaining a superposition of
> residue numbers in both subunits? In other workds: is there a possibility to
> leave some form of "chain identifier" in the .gro file? Or the only way to
> obtain unambiguous identification of each residue is to renumber the file?

There are no chain identifiers in .gro format.  If you want them, use .pdb 
instead.  You can make use of a variety of formats for just about all the 
Gromacs tools; there is no requirement for .gro.  If your input .pdb file has 
chain identifiers, so too should the output structure.

-Justin

> Thank you very much
> Anna
>  
> 
> Date: Fri, 13 May 2011 22:34:17 +1000
> From: Mark Abraham <mark.abraham at anu.edu.au>
> Subject: Re: [gmx-users] numbering of .gro file
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <7690ae4b5380.4dcdb1e9 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> 
> 
> On 13/05/11, Anna Marabotti  <anna.marabotti at isa.cnr.it> wrote:
>> Dear 
>> gmx-users,
>>
>> I'm simulating a 
>> homodimeric protein obtained by homology modelling. In the .pdb file, I
> have 2 
>> chain identifiers (A and B). I used Gromacs 4.0.7 to prepare the .gro
> files for 
>> simulation (up to nvt); then I was forced to switch to Gromacs 4.5.4 on
> another 
>> machine to continue with npt and full MD. I used the files from Gromacs
> 4.0.7 to 
>> continue, and it seems to me that all went OK. Now I have the files from
> the 
>> full MD, and I started to analyze them.
>>
>> I used g_rmsf to 
>> analyze the fluctuations of the residues, and I found that the results for
> the 
>> two subunits of the protein are superimposed. In the file .gro that comes
> from 
>> the MD as well as in the file .gro that comes from the npt MD made with
> Gromacs 
>> 4.5.4, the number of residues of the second subunit does not continue
> after the 
>> first subunit (i.e. after the last 359th residue of the first subunit, I
> see 
>> that the first residue of the second subunit is numbered 1 instead of
> 360), but 
>> in the nvt file produced by Gromacs 4.0.7 that I provided to Gromacs 
>> 4.5.4, the numbering of the two subunits is 
>> sequential. 
>>
>> My questions 
>> are:
>>
>> 1) why Gromacs 4.5.4 
>> changed the numbering of the residues in the two subunits, even if it
> started 
>> from a .gro file?
>>
>>
>>
>>
> 
> The trajectory files do not number the atoms, so the only way you can
> generate such numbering is by matching them with a structure file that also
> has such numbering. It's hard to be any more specific in the absence of
> command lines. If you just match the trajectory file with a more suitably
> numbered structure file (with atom ordering preserved) then everything is
> fine.
> 
> 
>>
>>
>>
>>
>> 2) Does this affect 
>> the result of the MD?
>>
>>
>>
>>
> 
> I highly doubt it.
> 
> 
>>
>>
>>
>>
>> 3) how can I 
>> separate, or renumber, the resulting .gro files in order to have a graph
> in 
>> which the fluctuations are not superimposed?
>>
>>
>>
>>
> 
> I rather expect that the input file to your NPT grompp had this "feature".
> In any case, you need to identify where it first arose in your workflow in
> order to work out why it happened and what to do about it.
> 
> Mark
> 
>>
>>
>>
>>
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-- 
========================================

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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