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 Sun Dec 01 2019 - 23:30:01 PST
