On Tue, 21 Mar 2017 20:56:48 +0000
Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk> wrote:
> > 2) I have two MD trajectories for a protein with protonated and
> > deprotonated glutamic acid. Simulations are run with AMBER, but the
> > parameters and topology are taken from CHARMM ff (we used chamber
> > tool to convert them to AMBER prmtop). I want to use a final
> > structure form one of them, for example the protonated one and do a
> > TI calculation on it without changing parameters (except
> > redistributing charges on deprotonated carbonyl group of course). In
> > the tutorial, AMBER ff is used to assign new charges:
> >
> > http://ambermd.org/tutorials/advanced/tutorial6/files/create_ash.leaprc
> >
> >
> > I am wondering if there is a way to do this step without using AMBER
> > ff?
>
> The TI code in sander/pmemd doesn't support the CHARMM force field.
Actually, I am not sure that this is true for sander so you maybe just
give it a try.
Cheers,
Hannes.
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Received on Wed Mar 22 2017 - 01:30:03 PDT
