Hi Clorice,
I think I'm going to follow your approach. It is the natural procedure in
fact.
It 's just that the changeProtState command is so useful... my laziness was
hoping it could work under a QM/MM scheme. :D
Thanks for your help!
David.
On Thu, Feb 6, 2020 at 8:27 PM Clorice Reinhardt <clorice.reinhardt.yale.edu>
wrote:
> Hi David,
>
> I can't address the dummy atom question, but alternatively I just
> parameterized the tyrosine residue in the deprotonated form following the
> RESP procedure for the 20 canonical amino acids, created a lib file, and
> ran MD from the get go with that. Which circumvents any issues with QM/MM
> and other simulations. I'm not sure your actual end goal here, so i can't
> say if this is the best plan of action for you-but that's how i proceeded.
>
> Clorice Reinhardt
>
>
> On Thu, Feb 6, 2020 at 5:39 PM David Sáez <davidsaez.udec.cl> wrote:
>
> > Hello everyone,
> >
> > I need a deprotonated TYR in my molecular dynamics simulation. I used
> > parmed > changeProtState as suggested in many posts. It worked well for
> the
> > MM part, but in the QM/MM section the software still "sees" the proton of
> > TYR (I think it became a dummy atom during the MM simulations). Is there
> a
> > way to keep it as a dummy atom?
> >
> > Thanks
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Received on Thu Feb 06 2020 - 19:00:02 PST
