[gmx-users] Re:mdrun_problem

Mark Abraham Mark.Abraham at anu.edu.au
Tue Aug 7 09:24:14 CEST 2007

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.


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