[gmx-users] Intermolecular Distance Restraints

[Kay Gottschalk]

It would be great to teach PyMol how to read Gromacs!
K.

On Aug 13, 2004, at 6:43 AM, Warren DeLano wrote:

> Hello,
>
> 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?
>
> Cheers,
> Warren
>
> --
> 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
Rehovot
Israel