AMBER Archive (2008)

Subject: RE: RE: AMBER: point charges

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri May 02 2008 - 18:03:08 CDT

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 |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu