AMBER Archive (2006)

Subject: Re: AMBER: regarding PBCAL in MM-PBSA

From: Ray Luo (rluo_at_uci.edu)
Date: Mon Oct 16 2006 - 19:35:42 CDT


Dear Jenk,

Please provide more information on your calculation. The statistics
output would be a good start.

Best,
Ray

Cenk Andac wrote:

> Dear Amber community,
>
> I was just wondering how one would go about interpretation of PBCAL
> values (in MMPBSA computations) for receptor and complex. PBCAL for my
> receptor has a more negative value than PBCAL for the complex. Does
> this mean that the complex experiences a lower dielectric lattice due
> to some water molecules replaced by the ligand in the binding site?
>
> best regards,
>
> jenk.
>
>
> ------------------------------------------------------------------------
> Yahoo! Messenger with Voice. Make PC-to-Phone Calls
> <http://us.rd.yahoo.com/mail_us/taglines/postman1/*http://us.rd.yahoo.com/evt=39663/*http://voice.yahoo.com>
> to the US (and 30+ countries) for 2/min or less.

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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