The atom name is "Mn" in your pdb and the mdread2.F90 entry has "MN".
This is giving the error
Best Regards
On Wed, 20 Nov 2019 at 17:16, Nisha Amarnath Jonniya <
phd1601271002.iiti.ac.in> wrote:
> Dear Sir,
>
>
> 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*
> else
> ! write( 0,* ) 'bad atom type: ',atype
> ! call mexit( 6,1 )
> x(l165-1+i) = 1.70 + 1.4;
> x(l170-1+i) = 0.51245;
> x(l175-1+i) = -0.15966;
> x(l180-1+i) = -0.00019781;
> x(l185-1+i) = 0.00016392;
> write(6,'(a,a)') 'Using carbon SA parms for atom type',
> atype
> end if
> end do ! i=1,natom
> !
> #############################
> and recompile it.
>
> But still same error comes while running decompose. Why bad atom type 'Mn'
> comes? but no where it is mentioned as 'Mn' instead "MN'.
>
> *ERROR*
> 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
> File "/home/parimal4/Software/amber18/bin/MMPBSA.py", 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
> 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
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
>
> "/home/parimal4/Software/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 157, in run
> self.prmtop))
> CalcError: /home/parimal4/Software/amber18/bin/sander failed with prmtop
> com0W.prmtop!
> Exiting. All files have been retained.
>
> On Tue, Nov 19, 2019 at 10:20 AM Nisha Amarnath Jonniya <
> phd1601271002.iiti.ac.in> wrote:
>
> > Dear David Sir,
> >
> > I used "source leaprc.water.tip3p" , "source leaprc.gaff2", "source
> > leaprc.protein.ff14SB". I have tried with closest water as well as
> without
> > water also but getting the same error while running the decompose free
> > energy. Do I need to load other leaprc for "MN"?
> >
> > *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...
> > 5001 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
> > File "/home/parimal4/Software/amber18/bin/MMPBSA.py.MPI", line 100, in
> > <module>
> > 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
> > 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
> > bad atom type: Mn
> > bad atom type: Mn
> > 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
> > 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
> > 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
> > File "/home/parimal4/Software/amber18/bin/MMPBSA.py.MPI", line 100, in
> > <module>
> > calc.run(rank, stdout=stdout, stderr=stderr)
> > File
> >
> "/home/parimal4/Software/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> > line 157, in run
> > calc.run(rank, stdout=stdout, stderr=stderr)
> > calc.run(rank, stdout=stdout, stderr=stderr)
> > File
> >
> "/home/parimal4/Software/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> > line 157, in run
> > self.prmtop))
> > CalcError: /home/parimal4/Software/amber18/bin/sander failed with prmtop
> > com_3W_7av_anp_mn.prmtop!
> > File
> >
> "/home/parimal4/Software/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> > line 157, in run
> > self.prmtop))
> > Error occured on rank 4.
> > Exiting. All files have been retained.
> > self.prmtop))
> > File "/home/parimal4/Software/amber18/bin/MMPBSA.py.MPI", line 100, in
> > <module>
> > CalcError: /home/parimal4/Software/amber18/bin/sander failed with prmtop
> > com_3W_7av_anp_mn.prmtop!
> >
> >
> > On Mon, Nov 18, 2019 at 6:06 PM David Case <david.case.rutgers.edu>
> wrote:
> >
> >> On Mon, Nov 18, 2019, Elvis Martis wrote:
> >>
> >> >Try adding the following lines in mdread2.F90 file (can be found here
> >> >AMBERHOME/Ambertools/src/sander) around line 1466 (before this line
> else
> >> > ! write( 0,* ) 'bad atom type: ',atype ! call mexit( 6,1 ))
> >> >else if (atype == 'MN') then
> >> > x(l165-1+i) = 1.69d0 + 1.4d0
> >> >
> >> >> bad atom type: Mn
> >>
> >> The error message indicates that the problem atom type is "Mn", not
> >> "MN". I suspect that the original fix was not really activated.(?)
> >>
> >> What leaprc.water files (or other leaprc files) did you load when you
> >> created the prmtop file? Use the printDetails action in parmed to
> >> examine you manganese ion to see what atom type it really has.
> >>
> >> Note that the "MN" in standard PDB files is used for both the atom name
> >> and the residue name. But PDB files don't have any information about
> >> atom *types*.
> >>
> >> ...good luck....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
> >
> >
>
> --
>
> Nisha Amarnath Jonniya
> PhD Research Scholar
> Biosciences and Biomedical Engineering
> Indian Institute of Technology, Indore
> India
> _______________________________________________
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Received on Wed Nov 20 2019 - 05:00:02 PST
