Hello
Could you send the prmtop files and just one of two frames (as rst) off the
list?
Best Regards
On Fri, 22 Nov 2019 at 10:00, Nisha Amarnath Jonniya <
phd1601271002.iiti.ac.in> wrote:
> Dear Sir,
>
> I tried changing the mdread2.F90 file with 'Mn"
>
> else if (atype == 'Mn') then x(l165-1+i) = 1.69d0 + 1.4d0*
>
> and recompiled and run.
>
> But the same error is coming.
> * in decom.in I am including MN residue number in "print_res="1-276".
>
>
>
>
> ############*ERROR*################
> Loading and checking parameter files for compatibility...
> sander found! Using /home/parimal4/Software/amber18/bin/sander
> cpptraj found! Using /home/parimal4/Software/amber18/bin/cpptraj
> Preparing trajectories for simulation...
> 100 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with /home/parimal4/Software/amber18/bin/sander
> calculating complex contribution...
> bad atom type: Mn
> bad atom type: Mn
> bad atom type: Mn
> File "/home/parimal4/Software/amber18/bin/MMPBSA.py.MPI", line 100, in
> <module>
> bad atom type: Mn
> File "/home/parimal4/Software/amber18/bin/MMPBSA.py.MPI", line 100, in
> <module>
> bad atom type: Mn
> File "/home/parimal4/Software/amber18/bin/MMPBSA.py.MPI", line 100, in
> <module>
> app.run_mmpbsa()
> File
>
> "/home/parimal4/Software/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> app.run_mmpbsa()
> File
>
> "/home/parimal4/Software/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> app.run_mmpbsa()
> File
>
> "/home/parimal4/Software/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> bad atom type: Mn
> bad atom type: Mn
> self.calc_list.run(rank, self.stdout)
> File
>
> "/home/parimal4/Software/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
>
>
>
>
> On Thu, Nov 21, 2019 at 7:37 PM David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Thu, Nov 21, 2019, Nisha Amarnath Jonniya wrote:
> > >
> > > I checked all my PDB files as well as pdf files from all trajectory,
> and
> > >"MN" is written everywhere and not "Mn".
> >
> > This is expected. Atom types are not recorded in PDB files.
> >
> > >But in complex.prmtop Mn2+ is showing.
> >
> > This is also expected.
> >
> > >and If I run decompose without MN it is running, giving no error.
> >
> > >> > I have added the lines as mentioned in mdread2.F90 file
> > >> >
> > >> > ########################3
> > >> > else if (atype == 'F') then
> > >> > x(l165-1+i) = 1.47d0 + 1.4d0
> > >> > x(l170-1+i) = 0.68563d0
> > >> > x(l175-1+i) = -0.1868d0
> > >> > x(l180-1+i) = -0.00135573d0
> > >> > x(l185-1+i) = 0.00023743d0
> > >> >
> > >> > *else if (atype == 'MN') then x(l165-1+i) = 1.69d0 +
> > 1.4d0*
> > ^^^^^
> >
> > If you have not done so, change "MN" here to "Mn", recompile, and see if
> > anything changes.
> >
> > ...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
>
> Nisha Amarnath Jonniya
> PhD Research Scholar
> Biosciences and Biomedical Engineering
> Indian Institute of Technology, Indore
> India
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>
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Received on Thu Nov 21 2019 - 21:00:02 PST
