Then use MMPBSA.py (note the .py at the end) from AmberTools 12, rather
than MMPBSA (the version from AmberTools 1.5).
Do you get the same error?
HTH,
Jason
On Wed, Jun 20, 2012 at 1:32 PM, qiqi <hova.1985.yahoo.com.cn> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> 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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AMBER mailing list
AMBER.ambermd.org
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Received on Wed Jun 20 2012 - 11:30:03 PDT
