Hi Jason,
Thank you very much for your help, the problem is solved.
However I met another problrm while running the example.
Here are the error message:
*******************************************************************
$AMBERHOME/bin/MMPBSA.py -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...
mmpbsa_py_energy found! Using /shared/build/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /shared/build/amber12/bin/cpptraj
Preparing trajectories for simulation...
50 frames were processed by cpptraj for use in calculation.
Beginning GB calculations with /shared/build/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with /shared/build/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
CalcError: /shared/build/amber12/bin/mmpbsa_py_energy failed with prmtop ras-raf.prmtop!
Exiting. All files have been retained.
*********************************************************
vi _MMPBSA_pb.mdin
PB
npbopt = 0
istrng = 0.1
bcopt = 5
inp = 2
accept = 0.001
cavity_offset = -0.5692
maxitn = 1000
fillratio = 4.0
iprob = 2.0
space = 0.5
eneopt = 2
dprob = 1.4
radiopt = 1
dbfopt = 1
epsin = 1.0
nfocus = 2
cutnb = 0
epsout = 80.0
fscale = 8
solvopt = 1
smoothopt = 1
sprob = 0.557
cavity_surften = 0.0378
************************************************************************
vi _MMPBSA_complex_pb.mdout.0
Reading parm file (ras-raf.prmtop)
title:
mm_options: e_debug=3
mm_options: ipb=2
mm_options: inp=2
mm_options: epsin=1.000000
mm_options: epsout=80.000000
mm_options: smoothopt=1
mm_options: istrng=100.000000
mm_options: radiopt=1
mm_options: dprob=1.400000
mm_options: iprob=2.000000
mm_options: npbopt=0
mm_options: solvopt=1
mm_options: accept=0.001000
mm_options: maxitn=1000
mm_options: fillratio=4.000000
mm_options: space=0.500000
mm_options: nfocus=2
mm_options: fscale=8
mm_options: bcopt=5
mm_options: eneopt=2
mm_options: cutnb=0.000000
mm_options: sprob=0.557000
mm_options: cavity_surften=0.037800
mm_options: cavity_offset=-0.569200
Processing ASCII trajectory (_MMPBSA_complex.mdcrd.0)
Processing frame 1
iter Total bad vdW elect nonpolar EPB frms
************************************************************
Anyone can help me or give me some advice.
Thanks
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2:08
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.ambermd.org
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Received on Fri Jun 22 2012 - 14:00:03 PDT
