AMBER Archive (2008)

Subject: Re: RE: AMBER: point charges

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Fri May 02 2008 - 17:42:18 CDT

Hi
Would you please explain more how to edit
individual residues / atoms in xleap and enter the charges for them?
I could not see the information in Tutorials.

CHRG : the atom charges. (Divide by 18.2223 to convert to charge
           in units of the electron charge)
what does this mean?

for example, point charge for N atom is -0.2 e.
I have to enter (-0.2) or (-0.2/18.2223)??

Thanks
Lin

----- Original Message -----
From: Ross Walker <ross_at_rosswalker.co.uk>
Date: Friday, May 2, 2008 2:37 pm
Subject: RE: AMBER: point charges
To: amber_at_scripps.edu

> Hi Lin,
>
> > Point charges are one of the force field parameters.
> > But, it seem not to be read on the frcmod file and prmtop file.
> >
> > Any other file can read and modify the point charge of the force
> field> parameters?
>
> Your question appears to be terribly confused. I'm not sure what
> exactly you
> are asking. If you mean how do you set the point charges for a
> residue these
> are contained in the residue templates read by leap. For example
> either a
> mol2 or prep file. These can be generated by antechamber. You can
> also edit
> individual residues in xleap and enter the charges there.
>
> Ultimately the charges end up in the prmtop file under the section
> %FLAGCHARGE
>
> These are the resp charges multiplied by 18.2223.
>
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
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