AMBER Archive (2009)

Subject: Re: [AMBER] method used to determine partial charges?

From: Jihang Wang (wangj3_at_mymail.vcu.edu)
Date: Thu Oct 01 2009 - 16:28:45 CDT

Thanks, Bill.
Actually I found the partial charges on amino acid residues, RNA, nucleic
acids etc in papers, and also as you said, in .lib files, but I could not
find the partial charges in some organic molecules, for example, the
nitrile group (-CN) I asked on the list a few days ago. Do you have any
suggestion about that? thanks again.

On Thu, Oct 1, 2009 at 5:19 PM, Bill Ross <ross_at_cgl.ucsf.edu> wrote:

> > I am curious to know which method is used to determine the partial charge
> > carried by atoms in the ff99 and glycam06 force fields? Are they
> Mulliken
> > charges?
>
> There are papers describing the derivation of each ff, including
> charge derivation. References should not be hard to find.
>
> > I wonder where can I find those partial charges?
>
> They are in the residue templates, I believe with .lib or .off extensions.
> In leap, 'desc <resname>' may show them.
>
> Bill
>
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