Am I doing anything wrong in generating those files?
Unable to locate the mistake.
On Wed, Feb 1, 2023 at 3:47 PM Ray Luo <rluo.uci.edu> wrote:
> That's why ... your water/ion-free crd and top files are inconsistent.
>
> 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 3:44 PM Suchetana Gupta
> <suchetana.gupta.gmail.com> wrote:
> >
> > 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
