Oops, I just realised I used the wrong mask for the ions.
Thanks a lot Ray for pointing this out.
It works now.
-Suchetana
On Wed, Feb 1, 2023 at 3:49 PM Suchetana Gupta <suchetana.gupta.gmail.com>
wrote:
> 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
>> >> >
>> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!KF4PXl7zJ90u7rM1MWqABdX46aw-lgUd8TC3de_B825VD4ildO4BgQBDp9C24aes5Ul-tl4Kyrm51A$
>>
>
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Received on Wed Feb 01 2023 - 16:30:03 PST
