[gmx-users] Intermolecular Distance Restraints
kay.gottschalk at weizmann.ac.il
Sun Aug 15 07:24:20 CEST 2004
It would be great to teach PyMol how to read Gromacs!
On Aug 13, 2004, at 6:43 AM, Warren DeLano wrote:
> I've finally learning some GROMACS and have been using it to
> 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
> 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
> least painful workaround?
> Would it be worthwhile teaching PyMOL how to visualize, manipulate, &
> 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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Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
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