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
>
>
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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 Thu Nov 21 2019 - 20:30:02 PST
