[gmx-users] numbering of .gro file

[Justin A. Lemkul]

Anna Marabotti 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 behavior in 4.0.7 was for pdb2gmx to always renumber the input coordinate 
file so that your resulting, processed coordinates started with residue 1 and 
proceeded sequentially.  For various reasons, people did not always want that, 
so in 4.5 the -renum flag was added and the default behavior was changed so that 
renumbering did not occur unless requested, and each chain was numbered 
independently of any previous chain.

> 2) Does this affect the result of the MD?

Numbering is irrelevant in the grand scheme.  Matching between coordinates and 
topology is the only requirement for proper interpretation of the structure.

> 3) how can I separate, or renumber, the resulting .gro files in order to 
> have a graph in which the fluctuations are not superimposed?

genconf -renumber will renumber your .gro file, but for proper mass-based 
analysis like RMSF, you need a .tpr file, which in this case still contains the 
chain information.  You can write a simple post-processing script to renumber 
the resulting .xvg file.

-Justin

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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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