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 - 17:42:38 CDT

Great, thanks a lot.

On Thu, Oct 1, 2009 at 6:30 PM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> Amber doesn't include partial charges, but it does include a program
> (antechamber) that calculates partial charges for various organic
> molecules. You could use this to generate a parameter set for
> simulations. There is quite a bit of info in the manuals and
> tutorials.
> http://ambermd.org/antechamber/antechamber.html
>
> On Thu, Oct 1, 2009 at 6:26 PM, Jihang Wang <wangj3_at_mymail.vcu.edu> wrote:
> > 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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