Dear Horn and Bill
Sorry for the late reply.
Thank you for your suggestion.
Best Regards
Aashish
On Mon, Dec 2, 2019 at 7:22 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> Have you read the relevant Amber ff papers for the charge derivation
> methods? If not, I would.
>
> Bill
>
> On 12/1/19 11:04 PM, Aashish Bhatt wrote:
> > Dear Amber user
> >
> > I have been trying to prepare force field parameter for a molecule which
> is
> > covalently bound with protein.
> > I have created ACE and NME group in the molecule to mimic the peptide
> > environment.
> > I have optimised molecule with -1 charge and when i delete the ACE and
> NME
> > groups the charge of the system was -0.7812.
> > I am getting confused if i can use the same charges of the atoms to
> create
> > force field parameters or some how try to balance the residual -0.2188
> > charges by manually distributing to certain atoms.
> >
> > Can you give me suggestions to deal with such systems?
> >
> >
> > Best Regards
> >
> > Aashish
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Received on Thu Dec 05 2019 - 04:30:02 PST
