[gmx-users] R: gmx-users Digest, Vol 85, Issue 101

[Anna Marabotti]

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?
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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