AMBER Archive (2008)

Subject: Re: AMBER: antechamber and gaff for a homodimer

From: FyD (
Date: Thu Nov 27 2008 - 10:02:55 CST

Quoting rebeca <>:

> Thank you for your answer. I have already done it. But I would like to see
> the difference between doing it with one monomer and the total dimer,
> because for example, the distribution of the charges is not the same and it
> would be affected by the hydrogen bonds formed between both monomers.
> Any idea?

Usually you avoid the conformation(s) with H-bond(s) when you derive
RESP charges (MEP computed with the HF/6-31G* theory level) because it
leads to over-polarization effect...

regards, Francois

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