[gmx-users] opla atom types and charges for nitrile / thienopyridine
kruggel at chemie.uni-hamburg.de
Fri Jan 29 14:51:49 CET 2010
i generated a lig.itp file with topolgen.pl to perform
ligand/protein md simulations. as my ligand contains
nitriles and a thienopyridine scaffold, topolgen failed
assigning atom types.
i found opls_753/4 in ffoplsaa.atp for the nitrile but
changing the *itp file i didn't find any hint for the charge
nor the chgr entry to put. additionally i am not sure about
the treatment of the pyridine nitrogen as i only see the
opls_520 and i don't know what the 6-31G* is meaning.
in the mailing list i found
but wondered if oplsaa shouldn't be the better choice for a
md simulation of ligand and protein - or is the gromos53a6
(or the gmx force field as used in the drug/enzyme tutorial
) not too bad?
maybe anybody has done simulations with similar molecules,
thanks in advance for any help!
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