Dear Clorice and Amber experts,
It is the first time I derive charges for a central nonnatural residue.
According to the paper of Cieplak 1995, it must be capped with ACE and NME,
and those residues have predefined charges.
Is there a way to keep the charges of ACE and NME fixed to the predefined
values during
the RESP fitting?
To the final .lib file I should only export the data regarding the central
residue, not ACE and NME, right?
Thanks!
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 Tue Feb 11 2020 - 07:30:01 PST
