You will find many FF libraries for more than 200 cofactors; GMP, GDP,
GTP are obviously available...
regards, Francois
> I am looking into starting simulations of a protein that has a GDP and a
> MG ion in the active site.
> I know that in the database of AMBER parameters there are the Carlson
> parameters for GDP and the new Sorensen parameters for MG.
>
> I also found this comment from David Case which made me wonder about
> GDP. Is there anything new on the paper mentioned there ?
> http://archive.ambermd.org/201112/0208.html >
> I also read carefully this thread.
> http://archive.ambermd.org/201205/0530.html >
> Before starting simulations, I would be very grateful if people that
> have been using these parameter sets would comment on their experience
> with them (besides what is published in the respective references).
>
> If people are aware of other parameter sets, not available in the data
> base but worth trying out, I would also be very interested.
>
> Best wishes
> Vlad
