Hi,
I am using Amber11 and I have already built the latest Ambertools.
Best wishes,
Angela
--- 12年6月21日，周四, Jason Swails <jason.swails.gmail.com> 写道：
发件人: Jason Swails <jason.swails.gmail.com>
主题: Re: [AMBER] Problem while running MMPBSA
收件人: "AMBER Mailing List" <amber.ambermd.org>
日期: 2012年6月21日,周四,上午1:19
Can you try upgrading to AmberTools 12 and try the version of MMPBSA.py
included there?
All the best,
Jason
On Wed, Jun 20, 2012 at 12:08 PM, qiqi <hova.1985.yahoo.com.cn> wrote:
> Hi all,
>
>
> I met a problem while runnin MMPBSA, even trying to run the tutorial
> examples.
> The error message are as followed.
> Can anyone give me some advice about how to solve this problem.
> Thanks.
>
>
> MMPBSA -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp ras.prmtop -lp raf.prmtop -y
> *.mdcrd
>
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> ptraj found! Using /shared/build/amber11/bin/ptraj
> mmpbsa_py_energy found! Using /shared/build/amber11/bin/mmpbsa_py_energy
> for GB calculations
> mmpbsa_py_energy found! Using /shared/build/amber11/bin/mmpbsa_py_energy
> for PB calculations
> Preparing trajectories for simulation...
> sh: line 1: 24583 Floating point exception/shared/build/amber11/bin/ptraj
> ras-raf.prmtop _MMPBSA_complexinpcrd.in > _MMPBSA_ptraj4.out 2>&1
> sh: line 1: 24589 Floating point exception/shared/build/amber11/bin/ptraj
> ras.prmtop _MMPBSA_receptorinpcrd.in > _MMPBSA_ptraj5.out 2>&1
> sh: line 1: 24591 Floating point exception/shared/build/amber11/bin/ptraj
> raf.prmtop _MMPBSA_ligandinpcrd.in > _MMPBSA_ptraj6.out 2>&1
> 2 frames were read in and processed by ptraj for use in calculation.
>
> Beginning GB calculations with mmpbsa_py_energy...
> calculating complex contribution...
> getpdb: can't open file _MMPBSA_complex.pdb
> Error: mmpbsa_py_energy error during GB calculations!
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
>
>
> Angela
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jun 20 2012 - 11:00:03 PDT
