AMBER Archive (2005)

Subject: Re: AMBER: mm_pbsa

From: Wei Chen (gtg553p_at_mail.gatech.edu)
Date: Fri Jul 29 2005 - 22:53:36 CDT

Hi, Liu

Thank you!

When I use serial sander, it works.

Everything is fine when I used files in Examples.
However, for my own molecular files, some errors happen:

/gt/lib1/Library/amber8/exe/pbsa -O -i pbsa.in -o pbsa_com.1.out -
c ./snapshots/hFc1_CD16B_na2_com.crd.1 -p ./hFc1_CD16B_na2_minimize.prmtop not
successful

It seems to be something wrong with pbsa. In pbsa_com.1.out:

 Grid dimension at level 1 37 49 53
 Grid origin corrected at level 1 -24.087 -65.371 -110.095
 Grid dimension at level 2 157 205 225
 Grid origin corrected at level 2 12.413 -16.871 -58.595
 PB bomb in pb_setgrd(): Allocation aborted 24*0, 2*4205, 4*0

Do you have any idea?

Wei Chen

ÒýÓÃ JunJun Liu <ljjlp03_at_gmail.com>:

> Hi, Chen
>
> It's easy to modify mm_pbsa.pl to use MPI. For example, modify the
> following line s in mm_pbsa_calceneent.pm
> $command = $r_pro->{"SANDER"} . " -O" .
> to
> $command = "mpirun -np 1" . $r_pro->{"SANDER"} . " -O" .
>
> Another more convenient way is to specify the serial SANDER program in
> mmpbsa.in input file.
> @PROGRAMS
> SANDER path_to_sander_serial
>
> You can search the archive for more detailed discussions. I hope this
> helps.
>
> Regards!
>
> Liu
>
> On Sat, 30 Jul 2005 09:09:13 +0800, Wei Chen <gtg553p_at_mail.gatech.edu>
> 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
> >
> >
> > 引用 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
> >> >
> >> > 寮曠�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
> >> >>
> >> >>
> >> >>
> >> >>
> >> -----------------------------------------------------------------------
> >> >> The AMBER Mail Reflector
> >> >> To post, send mail to amber_at_scripps.edu
> >> >> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >> >>
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> JunJun Liu
> >>
> >> College of Chemistry
> >> Central China Normal University
> >> WuHan 430079
> >> P.R. China
> >> -----------------------------------------------------------------------
> >> The AMBER Mail Reflector
> >> To post, send mail to amber_at_scripps.edu
> >> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >>
> >
> >
>
>
>
> --
> JunJun Liu
>
> College of Chemistry
> Central China Normal University
> WuHan 430079
> P.R. China
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> 

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