[gmx-users] about specbond

David van der Spoel spoel at xray.bmc.uu.se
Wed Apr 16 09:38:34 CEST 2008

Rui Li wrote:
> Dear all,
> I'm trying to run a simulation of a ligand bound to an enzyme.I make a specbond
> between ligand and residue, Is this bond proper for EM or MD simulation? What
> parameters are defined on it?
if grompp doesn't complain there are parameters for angles and bonds 
etc. Use gmxdump to find out which values.
> Thank you in advance!
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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