It doesn't appear that you're trying to run decomp analysis, since your
output file appears to be NAB output from mmpbsa_py_energy. In this case,
the advice on that thread does not apply. Can you zip up your _MMPBSA_*
files and attach them so we can take a look?
All the best,
Jason
On Mon, Jun 25, 2012 at 11:33 AM, qiqi <hova.1985.yahoo.com.cn> wrote:
> 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
> _______________________________________________
> 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
Received on Mon Jun 25 2012 - 10:30:03 PDT
