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 Mon Dec 02 2019 - 06:00:05 PST
