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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Received on Fri Nov 15 2019 - 22:30:02 PST
