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 - 17:26:24 CDT

Thanks again for your reply.
Actually, I'm just trying to do some simulations of -CN groups with
different force fields. So you are saying Amber ff only have partial charges
available for biological systems? since in OPLS-AA ff, I found the partial
charges for organic molecules too.

On Thu, Oct 1, 2009 at 6:18 PM, Bill Ross <ross_at_cgl.ucsf.edu> wrote:

> > I could not find the partial charges in some organic molecules,
> > for example, the nitrile group (-CN)
>
> If this is not a residue in the dbase, there wouldn't be charges
> for it per se. If it is a substituent of other residues, you
> could see how the charges vary per residue (I'm not a chemist,
> so not sure what you expect).
>
> Bill
>
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