hi justin,
thanks for the quick answer and ...
> Either way, parameterization is going to be hard.
so you don't think the use of default parameters of gmx-ff
as described in the drug-enzyme-tutorial to be useful (to
give reasonable results) if i want to get an impression of
the stability of docked poses and for the calculation of
binding free energies?
simulations don't crash the way described in
http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf
- i only thought that oplsaa would probably be the 'better
choice'?
thanks for your estimation,
sebastian
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Sebastian Kruggel
Institut für Pharmazie
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D 20146 Hamburg
Tel: +49 (0)40 42838-3626 (-3484)
mail: krug...@chemie.uni-hamburg.de
http://www.chemie.uni-hamburg.de/pha/phachem/lemcke/mitarbeiter.html
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