pkmukher wrote:
Hi users,
I am having a problem during the running of the mdrun
program on my prepared system.I have a system containing a
protein/peptide complex. i have prepared the protein using
the pdb2gmx utility and the peptide using the PRODRG
utility. I have then included the ligand .itp file into the
protein top file. when i run grommpp followed by mdrun I see
a translation of the peptide/protein complex in the output
structure file(also confirmed by looking at the actual pdb
file coordinates). Tranlation of a system to a new point
(e.g. center of solvent box) is a normal procedure and would
not effect calculations because the position of the peptide
and the protein within the complex would remain the same
relative to each other. However in this case i find that a
translation of the X coordinates has been performed for the
protein atoms while a translation of the Y and Z coordinates
has been performed for the peptide. This results in the
peptide moving outside of the binding site of the protein
i.e. the protein and the peptide are not placed at the same
place "relative to each other" as present in the input
structure file.I have included portions of the input and the
output structure files.
My comments from last time you posted this problem still apply...
http://www.gromacs.org/pipermail/gmx-users/2007-July/028877.html These
molecules will be in the same position modulo the size of the cell. I
note that you've given us some more information than last time, but
still haven't bothered to give us the size of the cell, like I asked
for. If you want people to respond helpfully, you need to respond
suitably to what they say.
thus the protein has been translated as [X,0,0]
while the peptide has been translated by [0,Y,Z]
The desired translation for protein is [X,Y,Z]
and the desired translation for the ligand is [X,Y,Z].
Who says this translation is desirable? Read up on trjconv and you can
convert this structure to one that suits your viewing needs.
Mark
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