[gmx-users] opla atom types and charges for nitrile / thienopyridine

[Sebastian Kruggel]

hello,

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
http://lists.gromacs.org/pipermail/gmx-users/2009-May/042069.html
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
http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf
) not too bad?

maybe anybody has done simulations with similar molecules, 
thanks in advance for any help!

sebastian



-- 
Sebastian Kruggel
Institut für Pharmazie
Bundesstr. 45 | Raum 112 (406)
D 20146 Hamburg

Tel:   +49 (0)40 42838-3626 (-3484)
mail:  kruggel at chemie.uni-hamburg.de
http://www.chemie.uni-hamburg.de/pha/phachem/lemcke/mitarbeiter.html