[gmx-users] Rigid body optimization
mhotchko at sdsc.edu
Thu Nov 27 01:07:01 CET 2003
I am trying to use Gromacs to analyze multiple configurations of a two
protein complex. I would like to set the structures with rigid bonds and
rigid angles, to make both of the proteins rigid bodies. I tried using
constraints = all-angles
in my md simulation .mdp file, but when I run grompp, I get the following
Fatal error: No bond information for bond H1-N or N-H2
What do I need to do in for processing my pdb file with pdb2gmx or what
else do I need to include in the md.mdp file to get rid of this problem?
Secondly, I would like to do a different MD simulation where only the
energy of the protein-protein interfaces/interactions is counted. I have
two proteins, labled chain E and chain I. I made an index file for these
two residues and then tried using the
energygrp_excl = chE chI
energygrps = chE chI
and even adding information for both tau_t and ref_t.
in my md.mdp, but, I keep getting errors in the process. What is the
process from pdb2mgx to mdrun for excluding internal protein energies, so
I can just look at interface energies.
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