AMBER Archive (2006)

Subject: Re: AMBER: quistions about pbsa cacultaion

From: snowyowls (amberlist_at_gmail.com)
Date: Tue Mar 14 2006 - 20:43:46 CST

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>:
>
> 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
> Home page: http://rayl0.bio.uci.edu/rayl/
> ====================================================
>
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