Hi
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
and recompile the AMBER.
Best Regards
On Mon, 18 Nov 2019 at 13:52, Nisha Amarnath Jonniya <
phd1601271002.iiti.ac.in> wrote:
> Dear Sir,
>
> Even I tried with Amber 16 also giving the following error. In my PDB "MN"
> is written in capital, Do I need to change it?
>
>
> *ERROR*
> ###############################################
> Beginning GB calculations with /apps/amber16/bin/sander
> calculating complex contribution...
> bad atom type: Mn
> File "/apps/amber16/bin/MMPBSA.py.MPI", line 100, in <module>
> app.run_mmpbsa()
> File "/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 157, in run
> self.prmtop))
> CalcError: /apps/amber16/bin/sander failed with prmtop
> com_a7y_anp_mn.prmtop!
> Error occured on rank 2.
> Exiting. All files have been retained.
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> bad atom type: Mn
> File "/apps/amber16/bin/MMPBSA.py.MPI", line 100, in <module>
> app.run_mmpbsa()
> File "/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 157, in run
> self.prmtop))
> CalcError: /apps/amber16/bin/sander failed with prmtop
> com_a7y_anp_mn.prmtop!
> Error occured on rank 0.
> Exiting. All files have been retained.
> bad atom type: Mn
> File "/apps/amber16/bin/MMPBSA.py.MPI", line 100, in <module>
> app.run_mmpbsa()
> File "/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 157, in run
> self.prmtop))
> CalcError: /apps/amber16/bin/sander failed with prmtop
> com_a7y_anp_mn.prmtop!
> Error occured on rank 1.
> Exiting. All files have been retained.
> bad atom type: Mn
> File "/apps/amber16/bin/MMPBSA.py.MPI", line 100, in <module>
> app.run_mmpbsa()
> File "/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 157, in run
> self.prmtop))
>
> On Mon, Nov 18, 2019 at 11:38 AM Elvis Martis <elvis_bcp.elvismartis.in>
> wrote:
>
> > Helio
> > What is the error this time??
> > Best Regards
> >
> >
> >
> > On Sun, 17 Nov 2019 at 08:24, Nisha Amarnath Jonniya <
> > phd1601271002.iiti.ac.in> wrote:
> >
> > > Thank you Sir,
> > > I am using Amber 18 for running the calculation but still getting the
> > error
> > > as it was mentioned to use update version of Amber in the link.
> > >
> > >
> > > On Sat, 16 Nov 2019, 11:52 am Elvis Martis, <elvis_bcp.elvismartis.in>
> > > wrote:
> > >
> > > > Hi
> > > > It seems the MMPBSA.py failed because of the Mn atom.
> > > > Look at this previous post for a fix
> > > > http://archive.ambermd.org/201412/0132.html.
> > > > After making the said changes you will have to recompile AMBER serial
> > > > version
> > > > Best Regards
> > > >
> > > >
> > > >
> > > > On Sat, 16 Nov 2019 at 11:31, Nisha Amarnath Jonniya <
> > > > phd1601271002.iiti.ac.in> wrote:
> > > >
> > > > > Hello Amber Users,
> > > > > I am running cmd simulation of the complex with the ligand
> including
> > > ANP
> > > > > and Mn for the kinase. Strange thing happen is that while
> calculating
> > > > > MMPBSA and nmode calculations no error comes but in case of
> decompose
> > > of
> > > > > binding free energy calculation using MMGBSA following errors comes
> > > > > although I have used the same prmtop and .mdcrd files for all the
> > > cases.
> > > > >
> > > > >
> > > > > *Input for decompose is:*
> > > > > Input file for running PB and GB
> > > > > &general
> > > > > endframe=20000, verbose=1,
> > > > > interval=10, keep_files=0,
> > > > > startframe=6000,
> > > > > /
> > > > > &gb
> > > > > igb=2, saltcon=0.100,
> > > > > /
> > > > > &decomp
> > > > > idecomp=1, dec_verbose=1,
> > > > > print_res="1-276",
> > > > > /
> > > > > ########################
> > > > > *ERROR*
> > > > > CalcError: /home/Software/amber18/bin/sander failed with prmtop
> > > > > com_anp.prmtop!
> > > > > Error occured on rank 3.
> > > > > Exiting. All files have been retained.
> > > > > bad atom type: Mn
> > > > > File "/home/Software/amber18/bin/MMPBSA.py.MPI", line 100, in
> > > <module>
> > > > > app.run_mmpbsa()
> > > > > File
> > > > >
> > >
> "/home/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/Software/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> > > > > line 82, in run
> > > > > calc.run(rank, stdout=stdout, stderr=stderr)
> > > > > File
> > > > >
> > > > >
> > > >
> > >
> >
> "/home/Software/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> > > > > line 157, in run
> > > > > self.prmtop))
> > > > > CalcError: /home/Software/amber18/bin/sander failed with prmtop
> > > > > com_anp.prmtop !
> > > > > Error occured on rank 1.
> > > > > Exiting. All files have been retained.
> > > > > ######################################
> > > > >
> > > > > Any suggestions or help will be appreciated.
> > > > >
> > > > > Regards
> > > > >
> > > > > --
> > > > >
> > > > > 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
> > > > >
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> >
>
>
> --
>
> Nisha Amarnath Jonniya
> PhD Research Scholar
> Biosciences and Biomedical Engineering
> Indian Institute of Technology, Indore
> India
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Nov 18 2019 - 01:00:01 PST
