[gmx-users] Intermolecular Distance Restraints

Warren DeLano warren at delanoscientific.com
Fri Aug 13 05:43:22 CEST 2004


I've finally learning some GROMACS and have been using it to model/refine
some enzyme-substrate complexes.  I'd like to be able to build some
arbitrary distance constraints into the simulation, but that is starting to
look like a problem.  Here's the deal:

1) I've got two chains with different termini -- the enzyme needs to be
NH3+/COO-, but the substrate should be capped ACE/NAC.  In order to generate
a proper pdb2gmx topology with proper termini, it seems that the enzyme &
substrate need to be separate molecules.

2) According to some prior posts on the list, there is no way in GROMACS to
define the topology for intermolecular distance restraints.

I'm stuck.  Is there a general way around this?  If not, then what's the
least painful workaround?

Would it be worthwhile teaching PyMOL how to visualize, manipulate, & merge
GROMACS topologies?  


mailto:warren at delsci.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

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