AMBER Archive (2005)

Subject: Re: Re: AMBER: mm_pbsa

From: zgleo (zgleo_at_tom.com)
Date: Sun Jul 31 2005 - 10:26:02 CDT

Dear Wei Chen,

        You can compile sander into serial version by "make serial" instead of "make".

======= 2005-07-30 09:09:13 you wrote=======

>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
>
>
>ÒýÓÃ JunJun Liu <ljjlp03_at_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_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
>> >> >
>> >> > --
>> >> >
>> >> > ----------------------------------------------------------------------
>> >> > -
>> >> > The AMBER Mail Reflector
>> >> > To post, send mail to amber_at_scripps.edu
>> >> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>> >> >
>> >>
>> >>
>> >> ----------------------------------------------------------------------
>> >> 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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>> >> The AMBER Mail Reflector
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>> >>
>> >
>> >
>>
>>
>>
>> --
>> JunJun Liu
>>
>> College of Chemistry
>> Central China Normal University
>> WuHan 430079
>> P.R. China
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>> The AMBER Mail Reflector
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>>
>
>
>--
>
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= = = = = = = = = = = = = = = = = = = =
                        

Best regard!
 
                                 
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡zgleo
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2005-07-31

___________________________________________
    
Zhiguo Liu
Ph.D candidate
Drug Discovery and Design Center
Shanghai Institute of Materia Medica
Chinese Academy of Science
Shanghai, China
zhiguo.leo_at_gmail.com
___________________________________________

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