[gmx-users] Rigid body optimization
feenstra at chem.vu.nl
Thu Dec 4 09:14:02 CET 2003
Matthew Hotchko wrote:
> I sent a similar message and no one replied. I guess that means no one
> knows the answer. Just in case you missed it, here I go again.
Strange, I did send a reply. I'll paste the answer back in again,
and add some additional thoughts that have occurred to me...
> 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
constraints = all-angles is not often used, so you may have stumbled on
a bug here. Could anyone confirm whether all-angles constraints still
works (and with which FF's it works), or confirm that it indeed is shaky?
Another thing is that this does *not* make your protein really rigid,
just more rigid than it normally would be. There is no proper 'rigid body'
constraints algorithm implemented in Gromacs...
> 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
IIRC, energygrp_excl expects group *pairs*, and you'd want to exclude only
the self interactions, like:
energygrp_excl = chE chE chI chI
The other line you could leave as it is.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |
More information about the gromacs.org_gmx-users