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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> > >
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> >
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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 - 00:30:02 PST
