Thanks!
Ray
--
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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>
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Received on Sun Aug 18 2019 - 07:30:01 PDT