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 - 04:00:01 PST
