[gmx-users] opla atom types and charges for nitrile / thienopyridine
Justin A. Lemkul
jalemkul at vt.edu
Fri Jan 29 15:40:30 CET 2010
Sebastian Kruggel wrote:
> 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.
See below for parameterization advice. See the manual for information on charge
groups - the .atp file won't help you there.
> 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.
6-31G* is a QM charge calculation method often used in deriving parameters; see
> in the mailing list i found
The more applicable message in the thread above is actually the next message:
Virtual sites can be tricky with the nitrile group.
> 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?
Either way, parameterization is going to be hard. Please consult the following,
and consider that deriving parameters for any new species is a very advanced
topic and should only be undertaken with a thorough knowledge of derivation
procedures and the intrinsics of the desired force field:
You could certainly derive parameters suitable for either force field (OPLS or
53a6), but it will take a considerable amount of time. The topolgen.pl script
is just a cute little utility I wrote some time ago to give you a starting point
for topology generation. Its output should not necessarily be considered
accurate or appropriate for immediate simulation, anyway. You've got to do the
legwork of deriving parameters from there!
> maybe anybody has done simulations with similar molecules, thanks in
> advance for any help!
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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