[gmx-users] numbering of .gro file
Justin A. Lemkul
jalemkul at vt.edu
Fri May 13 14:30:41 CEST 2011
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 A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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