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
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> > >
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> >
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Received on Sun Nov 17 2019 - 22:30:02 PST
