AMBER Archive (2006)

Subject: Re: AMBER: quistions about pbsa cacultaion

From: Ray Luo (rluo_at_uci.edu)
Date: Wed Mar 15 2006 - 11:36:56 CST

If you use pbsa, then it's not used for anything.

snowyowls wrote:

> oh~
> i see
> thank you~~
> but i have another question
> what is the pqr file created during mm_pbsa caculation using for?
>
>
>
> 2006/3/13, Ray Luo < rluo_at_uci.edu <mailto:rluo_at_uci.edu>>:
>
> pbsa doesn't use your pqr file, it uses your prmtop file for
> charges and
> radii.
>
> > dear all amber user:
> > right now i have run a pbsa caculation
> > in th input file of mm_pbsa
> > i using the parm set as PROC=1 it means i use the pbsa program
> of the
> > amber suite
> >
> > then i find that there are something abnormality in pqr files
> > there are no charge infomations, pqr file turn to a pr file,
> > hehe
>
> --
> ====================================================
> 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 <mailto:rluo_at_uci.edu>
> Home page: http://rayl0.bio.uci.edu/rayl/
> ====================================================
>
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-- 
====================================================
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/
====================================================

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