Re: [AMBER] MMGBSA and MMPBSA error (CalcError: failed with prmtop file complex.prmtop!)

From: Ray Luo <rluo.uci.edu>
Date: Sun, 5 Jul 2020 11:31:34 -0700

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
> >
> _______________________________________________
> 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
Received on Sun Jul 05 2020 - 12:00:03 PDT
Custom Search