AMBER Archive (2008)

Subject: Re: RE: RE: AMBER: point charges

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Sat May 03 2008 - 16:47:23 CDT

Hi
This is an example of prepin file in the ..../dat/leap/prep
Would you please explain about the meanings the three charge terms?

Thank you
Lin

 NHE INT 1
 CORRECT OMIT DU BEG
   0.00000
   1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000
   2 DUMM DU M 1 0 -1 1.0000 0.0000 0.0000
   3 DUMM DU M 2 1 0 1.0000 90.0000 0.0000
   4 N N M 3 2 1 1.3350 116.6000 180.0000
   5 HN1 H E 4 3 2 1.0100 119.8000 0.0000
   6 HN2 H E 4 3 2 1.0100 119.8000 180.0000
    
CHARGE
  -0.46300 0.23150 0.23150
    

----- Original Message -----
From: Ross Walker <ross_at_rosswalker.co.uk>
Date: Friday, May 2, 2008 4:05 pm
Subject: RE: RE: AMBER: point charges
To: amber_at_scripps.edu

> Hi Lin
>
> > 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.
>
> Try this tutorial:
>
> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four_orig/
>
> > 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)??
>
> No -0.2 e is correct. However if you look in the prmtop file you
> will see it
> is stored in there as -3.64446. Hence if you are looking at values
> in the
> prmtop file you need to divide these by 18.2223 to get the values in
> electrons (or the values you would use in leap.)
>
> Good luck,
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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