[gmx-users] ProDrg

Magnus Lundborg magnus.lundborg at scilifelab.se
Wed Dec 10 10:00:59 CET 2014

Dear Yao,

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?
> Thanks,
> Yao

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