AMBER Archive (2004)

Subject: Re: AMBER: Questions about pert.charge and atom type change.

From: David A. Case (case_at_scripps.edu)
Date: Wed Jun 30 2004 - 20:10:02 CDT

On Wed, Jun 30, 2004, Chunhu Tan wrote:
>
> I am trying to do TI with sander, but I am still confused with the
> pert.charge in xleap. My question is, when a H (with the charge 0.0791)
> atom becomes a dummy, if its pert.charge is 0-0.0791=-0.0791? If this
> is true, why the dummy H atoms on this page have no pert.charge?

> http://web.njit.edu/all_topics/Prog_Lang_Docs/html/amber7/gibbs_box/HTML/xleap_edit_selected.html

This is a mirror of quite an old page. The way in which perturbation charges
are entered changed from Amber7 to Amber 8. Please see the discussion on
pp. 33-34 of the Amber8 Users' Manual.

Don't be afraid to try things out. You know the beginning and ending charges
that you want (presumably), so just make sure that your prmtop file ends up
with the correct values. You can look at this file with an editor, or use
the rdparm program to help you out.

...regards...dac

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