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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Received on Sat Nov 16 2019 - 19:00:02 PST
