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 - 22:00:02 PST
