Hi Ray
Thanks for getting back to me.
I did check the output files and one shows this error:
FATAL: NATOM mismatch in coord and topology files
I am trying to understand why this is happening.
I generated the top files using ante-MMPBSA
ante-MMPBSA.py -p wt_wat.top -c complex.top -r rec.top -l lig.top -n
:199-205 -s :WAT,Na+
On Wed, Feb 1, 2023 at 3:41 PM Ray Luo <rluo.uci.edu> wrote:
> Suchetana ,
>
> Have you got a chance to review the output files as suggested?
>
> 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 Wed, Feb 1, 2023 at 2:50 PM Suchetana Gupta via AMBER
> <amber.ambermd.org> wrote:
> >
> > Dear Amber Users
> > I need help in diagnosing an error with MMGBSA.
> > When I try to run an MMGBSA analysis on a trajectory (the trajectory
> looks
> > absolutely fine on VMD and inspection in a text editor also shows no
> > issues), I get the following error:
> >
> > MMPBSA.py -O -i mmgbsa1.in -sp wt_wat.top -cp complex.top -rp rec.top
> -lp
> > lig.top -y imaged1.crd -o mmgbsa1.dat -do decomp1.dat > mmgbsa1.out &
> > [1] 23047
> >
> >
> > (ambertools-20220513) [sugupta.n099 water-md]$ File
> > "/packages/miniconda/20190102/envs/ambertools-20220513/bin/MMPBSA.py",
> line
> > 100, in <module>
> > app.run_mmpbsa()
> >
> >
> > File
> >
> "/packages/miniconda/20190102/envs/ambertools-20220513/lib/python3.10/site-packages/MMPBSA_mods/main.py",
> > line 218, in run_mmpbsa
> > self.calc_list.run(rank, self.stdout)
> >
> >
> > File
> >
> "/packages/miniconda/20190102/envs/ambertools-20220513/lib/python3.10/site-packages/MMPBSA_mods/calculation.py",
> > line 82, in run
> > calc.run(rank, stdout=stdout, stderr=stderr)
> >
> >
> > File
> >
> "/packages/miniconda/20190102/envs/ambertools-20220513/lib/python3.10/site-packages/MMPBSA_mods/calculation.py",
> > line 156, in run
> > raise CalcError('%s failed with prmtop %s!' %
> > (self.program,
> >
> > CalcError:
> > /packages/miniconda/20190102/envs/ambertools-20220513/bin/sander failed
> > with prmtop complex.top!
> >
> >
> >
> > Fatal Error!
> >
> >
> > All files have been retained for your error
> > investigation:
> >
> > You should begin by examining the output files of the
> > first failed calculation.
> >
> > Consult the "Temporary Files" subsection of the MMPBSA.py chapter
> in
> > the
> >
> manual
> > for file naming conventions.
> >
> >
> >
> >
> > [1]+ Exit 1
> > MMPBSA.py -O -i mmgbsa1.in -sp wt_wat.top -cp complex.top -rp rec.top
> -lp
> > lig.top -y imaged1.crd -o mmgbsa1.dat -do decomp1.dat > mmgbsa1.out
> > (ambertools-20220513) [sugupta.n099
> > water-md]$
> >
> >
> > The mmgbsa input that I am using is:
> >
> > MMPBSA.py input file for running GB
> >
> > &general
> >
> >
> > startframe=1,
> > endframe=500, interval=100,
> >
> > keep_files=0, netcdf=1,
> >
> >
> > /
> >
> >
> > &gb
> >
> >
> > igb=5, saltcon=0.1
> >
> > /
> >
> >
> > &decomp
> >
> >
> > idecomp=4, dec_verbose=0,
> csv_format=0
> >
> >
> >
> > Please help me solve this.
> >
> > Have never ever faced this issue earlier and the system is a very simple
> > one with HIV-1 Protease and a natural substrate (so no forcefield issues
> > too)
> >
> > Thanks
> > Suchetana
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
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Received on Wed Feb 01 2023 - 16:00:03 PST
