Thank so much Prof Luo,
It worked in single CPU without MPI.
Thanks.
Best regards,
Nadaafiva
Pada tanggal Sen, 6 Jul 2020 pukul 01.32 Ray Luo <rluo.uci.edu> menulis:
> Nadaafiva,
>
> My suggestion is first to follow the standard approach, stripping all
> water and counter ions from your MD simulations. If your divalent ion
> is part of a residue topology, do not remove it. Make sure your
> trajectory and prmtop files are consistent by visualizing them on VMD.
>
> Next run a small job with a few frames only without MPI. See whether
> you can run the job on a single CPU.
>
> Finally please use the latest Amber (2020) release for your job ...
> You are using a four years old release. There are many bug fixes and
> upgrades during the last four years.
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor of Structural Biology/Biochemistry/Biophysics,
> Chemical and Materials Physics, Chemical and Biomolecular Engineering,
> Biomedical Engineering, and Materials Science and Engineering
> Department of Molecular Biology and Biochemistry
> University of California, Irvine, CA 92697-3900
>
> On Sat, Jul 4, 2020 at 8:18 PM Nada Afiva <nadaafiva.gmail.com> wrote:
> >
> > Dear list,
> > I am guessing the error was caused by Mn2+ ion.
> > I previously performed MD simulation with Mn2+ ion as part of receptor
> > along with DNA, and
> > I got netCDF file after stripping water, Na+ and Cl- ions.
> > Can I reorder the Mn2+ position in the trajectory file so that the ion is
> > placed after ligand.
> > I want to perform mmpbsa calculation after removing the Mn2+ along with
> > water, Na and Cl ions.
> > Please correct me if my understanding is wrong.
> > Thank you.
> > Best regards,
> > Nadaafiva
> >
> >
> > Pada tanggal Min, 5 Jul 2020 pukul 04.58 Nada Afiva <nadaafiva.gmail.com
> >
> > menulis:
> >
> > > Dear Amber list,
> > > I was performing MMGBSA and MMPBSA binding energy calculations.
> > > My system consisted of protein + DNA (555 residues), one Mn2+ ion, and
> > > ligand, so the complex contains 557 residues.
> > > I use NetCDF trajectory file after stripping out water, Na+, and Cl-
> ions
> > > I obtained complex, receptor, and ligand topologies using ante-MMPBSA.
> > >
> > > ante-MMPBSA.py -p complex01.prmtop -c complex.prmtop -s '!:1-557' -r
> > > receptor.prmtop -m :1-556 -l ligand.prmtop
> > >
> > > I used AmberTools16, but then I encountered the error below:
> > > CalcError: /home/amber16/bin/cpptraj failed with prmtop file
> > > complex.prmtop!
> > > Error occurred on rank 1.
> > >
> > > Attached is my input file and output files.
> > > I looked into _MMPBSA_complex_gb.mdout.1, but it said nothing about the
> > > error.
> > >
> > > Command to perform mmgbsa and mmpbsa:
> > > mpirun -np 2 MMPBSA.py.MPI -O -i mmpbsa1.in -cp complex.prmtop -rp
> > > receptor.prmtop -lp ligand.prmtop -y nowat.prod.nc -o final.dat
> > >
> > > If you have any suggestions, please help me.
> > >
> > > Best regards,
> > > Nadaafiva
> > >
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Received on Mon Jul 06 2020 - 14:30:02 PDT
