Hi,
I found a similar problem in the mailing list:
http://archive.ambermd.org/201206/0122.html
The suggestion is :" remove the dec_verbose variable from the MMPBSA_pb.mdin
file and then re-run the MMPBSA.py command line with the -use-mdins flag at
the end"
However, I didn't find the dec_verbose variable in my _MMPBSA_pb.mdin file.
I tried to found out which subroutine is wrong. I just found the error messages as in my last mail:
CalcError: /shared/build/amber12/bin/mmpbsa_py_energy failed with prmtop
ras-raf.prmtop!
Processing ASCII trajectory (_MMPBSA_complex.mdcrd.0)
Processing frame 1
iter Total bad vdW elect nonpolar EPB frms
By the way, I am using Ambertools12 and Amber11.
It will be great if you could give some more advice to solve the problem.
Thank you very much!
Best,
Angela
--- 12年6月23日，周六, 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23日,周六,上午7:26
Usually when PB quits, there is some kind of error message about what
subroutine it bombed out in. Do you see any information like that?
Without this information we will probably not be able to help.
All the best,
Jason
On Fri, Jun 22, 2012 at 4:33 PM, qiqi <hova.1985.yahoo.com.cn> wrote:
> 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
> _______________________________________________
> 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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Received on Mon Jun 25 2012 - 09:00:03 PDT
