magnus.lundborg at scilifelab.se
Wed Dec 10 10:00:59 CET 2014
STaGE is a new tool developed for generating parameters for small
molecules in GAFF, OPLS-AA and CGenFF, using external tools (e.g. ACPYPE
and MATCH). As Justin points out you should be very careful to check
that the parameters are right, but that might not be possible if you
need to generate parameters for many thousands of compounds, in which
case you should be aware of the risk of errors in the results instead
(after the simulations carefully check the parameters of compounds that
gave rise to interesting results).
STaGE is described in
http://pubs.acs.org.ezp.sub.su.se/doi/abs/10.1021/jp505332p . I can try
to help you if you run into problems (documentation can still be improved).
On 12/08/2014 08:12 PM, xy21hb wrote:
> Dear all,
> Since Justin mentioned in previous mails that PRODRG is almost unreliable,
> is there any reliable source for patching a new small molecule for gromacs, in general?
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