[AMBER] Charge distribution in molecule

From: Aashish Bhatt <aashish.ph16221.inst.ac.in>
Date: Mon, 2 Dec 2019 12:34:21 +0530

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
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

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Received on Sun Dec 01 2019 - 23:30:01 PST
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