Re: [AMBER] Error in MMPBSA calculation

--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical Physics, Biomedical Engineering, and Chemical Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Sun, Aug 18, 2019 at 10:58 AM Lei Zhao <jackyzhao010.gmail.com> wrote:
>
> Hi Ray,
> I have solved this problem by using MPICH-3.1.4. I recommend that you can test MMPBSA calculation by MMPBSA.py first.
>
> Regards,
>
> Lei
>
>
> > 在 2019年8月17日，下午9:21，rluo.uci.edu 写道：
> >
> >
> >   Lei,
> >   Can you email me a test case , off the list, for me to take a look?
> >   All the best,
> >   Ray Luo, Ph.D.
> >   rayluo.rayluolab.org
> >
> >   -------- Original Message --------
> >   Subject: Re: [AMBER] Error in MMPBSA calculation
> >   From: jacky zhao
> >   To: amber
> >   CC:
> >
> >     Actually, I have found this error again.  Our previous trajectory can be
> >     calculated by MMPBSA.py.MPI without any problem in previous version of
> >     amber18.  Recently, I have updated to the latest version of amber18 and
> >     amber19. This error can be encountered.
> >     Anyone can help me?
> >     Thank you very much.
> >     Regards,
> >     Lei
> >>        å¨        2019å¹´8æ16æ¥ï¼ä¸å4:14ï¼shivangi        agarwal
> >     <shiviagarwalpharma.gmail.com> åéï¼
> >>
> >> Hello all
> >>
> >> I want to calculate MMGBSA from dcd file. I have converted it to .mdcrd
> >> using cpptraj.
> >>
> >> cpptraj -p complex-box.prmtop -y sim1_14.dcd -x sim1_14_complex.mdcrd
> >> Then using,
> >>
> >> MMPBSA.py -i mmpbsa.in -o FINAL_RESULTS_MMPBSA_20_frames.dat  -sp
> >> complex-box.prmtop  -cp  complex.prmtop  -rp receptor.prmtop -lp
> >     ligand.prmtop
> >> -y sim1_14_complex.mdcrd
> >>
> >> ###MMPBSA.in#############
> >>
> >> Input file for running PB and GB in serial
> >> &general
> >>  endframe=20, keep_files=2,
> >> /
> >> &gb
> >> igb=2, saltcon=0.100,
> >> /
> >> &pb
> >> istrng=0.100,
> >> /
> >> ################################
> >>
> >> But getting error,
> >>
> >> Reading command-line arguments and input files...
> >> Loading and checking parameter files for compatibility...
> >> mmpbsa_py_energy found! Using
> >     /opt/apps/amber/amber12/bin/mmpbsa_py_energy
> >> cpptraj found! Using /opt/apps/amber/amber12/bin/cpptraj
> >> Preparing trajectories for simulation...
> >> 20 frames were processed by cpptraj for use in calculation.
> >>
> >> Beginning GB calculations with
> >     /opt/apps/amber/amber12/bin/mmpbsa_py_energy
> >> calculating complex contribution...
> >> calculating receptor contribution...
> >> calculating ligand contribution...
> >>
> >> Beginning PB calculations with
> >     /opt/apps/amber/amber12/bin/mmpbsa_py_energy
> >> calculating complex contribution...
> >> CalcError: /opt/apps/amber/amber12/bin/mmpbsa_py_energy failed with
> >     prmtop
> >> complex.prmtop!
> >> Exiting. All files have been retained.
> >>
> >> Can someone suggest?
> >>
> >> Regards
> >> Shivangi Agarwal
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