Re: AMBER: mm_pbsa

From: Wei Chen <gtg553p.mail.gatech.edu>
Date: Fri, 29 Jul 2005 21:09:13 -0400

Hi, Liu,

I am a new user for amber. Do you know how to modify mm_pbsa.pl or
use serial SANDER?

Thank you!

Wei Chen


JunJun Liu <ljjlp03.gmail.com>:

> Dear Chen:
>
> if you didn't modify the mm_pbsa.pl script to use MPI, I think you need to
> use the single processor version of SANDER.
>
> regards!
>
> Liu
>
> On Sat, 30 Jul 2005 08:55:07 +0800, Wei Chen <gtg553p.mail.gatech.edu>
> wrote:
>
> > Hi,
> >
> > I even got samder_com.1.out file. I think maybe somthing wrong with
> > mpirun.
> >
> > Thanks!
> >
> > Wei Chen
> >
> > 引用 Suxin Zheng <sxzheng.u.washington.edu>:
> >
> >> You should look the sander_com.1.out to see the problem, whether the
> >> top or the crd file is fited correctly.
> >>
> >> On Jul 29, 2005, at 5:10 PM, Wei Chen wrote:
> >>
> >> > Hi,
> >> >
> >> > When I ran mm_pbsa.pl xxx in amber8, some errors occur as follow:
> >> >
> >> > mpirun must be used to launch all MPI applications
> >> > /gt/lib1/Library/amber8/exe/sander -O -i sander_com.in -o
> >> > sander_com.1.out -
> >> > c ./hFc1_CD16B_na2_com.crd.1 -p ./hFc1_CD16B_na2_minimize.prmtop
> >> > not successful
> >> >
> >> > Anybody knows how to solve this problem?
> >> >
> >> > Wei Chen
> >> >
> >> > --
> >> >
> >> > ----------------------------------------------------------------------
> >> > -
> >> > The AMBER Mail Reflector
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> >> >
> >>
> >>
> >> ----------------------------------------------------------------------
> >> Suxin Zheng
> >> Research Associate
> >> Box 351700
> >> Department of Chemistry, University of Washington
> >> Seattle, WA, 98195-1700
> >> sxzheng.u.washington.edu
> >>
> >>
> >>
> >> -----------------------------------------------------------------------
> >> The AMBER Mail Reflector
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> >>
> >
> >
>
>
>
> --
> JunJun Liu
>
> College of Chemistry
> Central China Normal University
> WuHan 430079
> P.R. China
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
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Received on Sat Jul 30 2005 - 02:53:00 PDT
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