AMBER Archive (2003)

Subject: Re: electrostatic interaction energ. /delphi

From: Natasja Brooijmans (nbrooij_at_itsa.ucsf.edu)
Date: Tue Jun 24 2003 - 14:45:22 CDT

See this paper by Sheinerman and Honig:

J Mol Biol. 2002 Apr 19;318(1):161-77

Best,

Natasja

Natasja Brooijmans, Ph.D.
Visiting Post-Doctoral Scholar
Kuntz Laboratory
Department of Pharmaceutical Chemistry
University of California, San Francisco
San Francisco, CA 94143-2240
phone: 415-476 3986
fax: 415-502 1411
e-mail: nbrooij_at_itsa.ucsf.edu

On Tue, 24 Jun 2003, Tommi Kajander wrote:

> Hello,
> Would anybody know how i should provide
> data (partial charges) in DELPHI (sorry if this is
> bit misplaced..) if i wish to calculate the contribution
> of a single residue/group to interaction (binding).
>
> ie should i have only the charge on this atom to get the
> potential --but how do i get the free energies at
> the remote sites (if they are not charged..??? do
> i put these charges to the frc input file??)
>
> has anybody done this?
>
> Thanks,
> Tommi Kajander
>
>