Dear Sir,
I checked all my PDB files as well as pdf files from all trajectory, and
"MN" is written everywhere and not "Mn".
But in complex.prmtop Mn2+ is showing.
and If I run decompose without MN it is running, giving no error.
Strange thing is that, MMGBSA is running with MN without any error but if I
run decompose with same MN, it's giving error as bad atom type.
Thanks
On Wed, Nov 20, 2019 at 6:28 PM Elvis Martis <elvis_bcp.elvismartis.in>
wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> 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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Received on Wed Nov 20 2019 - 23:00:02 PST
