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
--
========================================
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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