[gmx-users] Rigid body optimization

[Anton Feenstra]

Matthew Hotchko wrote:

> 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 
> error.  
> 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.  

IIRC, energygrp_excl expects group *pairs*, and you'd want to exclude only
the self interactions, like:
energygrp_excl = chE chE chI chI


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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