Hi,
I have a protein-ligand system in which my ligand has an iodine atom type,
and I keep getting this error message when running MMPBSA.py
Beginning GB calculations with
/global/common/cori/software/amber/14/hsw/bin/sander
calculating complex contribution...
bad atom type: i
File "/global/common/cori/software/amber/14/hsw/bin/MMPBSA.py", line 104,
in <module>
app.run_mmpbsa()
File
"/global/common/cori/software/amber/14/hsw/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/global/common/cori/software/amber/14/hsw/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/global/common/cori/software/amber/14/hsw/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /global/common/cori/software/amber/14/hsw/bin/sander failed with
prmtop ache-ligand8.prmtop!
Exiting. All files have been retained.
Any ideas how to resolve this? I’ve tried different igbs and none work. Ive
used mbondi2, using amber18. Ive attached my directory.
MMGBSA.tar
<
https://drive.google.com/file/d/1SCto2D58bDW-hL_E9orNzr1s1aVh8Z5W/view?usp=drive_web>
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Received on Sun Sep 08 2019 - 13:00:02 PDT
