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
>
>
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>
--
Nisha Amarnath Jonniya
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
India
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Received on Mon Nov 18 2019 - 21:00:01 PST
