AMBER Archive (2005)

Subject: Re: AMBER: mm_pbsa

From: JunJun Liu (ljjlp03_at_gmail.com)
Date: Fri Jul 29 2005 - 19:58:53 CDT

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_at_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_at_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
>> >
>> > --
>> >
>> > ----------------------------------------------------------------------
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>>
>>
>> ----------------------------------------------------------------------
>> Suxin Zheng
>> Research Associate
>> Box 351700
>> Department of Chemistry, University of Washington
>> Seattle, WA, 98195-1700
>> sxzheng_at_u.washington.edu
>>
>>
>>
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>>
>
> 

-- 
JunJun Liu

College of Chemistry
Central China Normal University
WuHan   430079
P.R. China
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