Hi all,
My protein in protein-ligand complex contains zinc. I am running energy decomposition calculations with Amber 12 and Ambertools 17 for protein-ligand binding free energy. But when I want to decompose energy on per residue basis using &decomp namelist, it crashes with message
Loading and checking parameter files for compatibility...
File "/opt/amber16/bin/MMPBSA.py", line 98, in <module>
app.loadcheck_prmtops()
File "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 574, in loadcheck_prmtops
FILES.receptor_prmtop, FILES.ligand_prmtop)
File "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py", line 98, in __init__
self.complex_prmtop = LoadParm(complex_prmtop)
File "/opt/amber16/lib/python2.7/site-packages/parmed/amber/readparm.py", line 70, in LoadParm
parm = parm.view_as(AmberParm)
File "/opt/amber16/lib/python2.7/site-packages/parmed/amber/amberformat.py", line 426, in view_as
return cls.from_rawdata(self)
File "/opt/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py", line 266, in from_rawdata
inst.initialize_topology()
File "/opt/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py", line 218, in initialize_topology
self.load_structure()
File "/opt/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py", line 510, in load_structure
self._check_section_lengths()
File "/opt/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py", line 1284, in _check_section_lengths
check_length('ATOMIC_NUMBER', natom, False)
File "/opt/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py", line 1273, in check_length
(key, len(self.parm_data[key]), length))
AmberError: FLAG ATOMIC_NUMBER has 27959 elements; expected 3333
Exiting. All files have been retained.
We found a similar message in
http://archive.ambermd.org/201606/0168.html , but it was unanswered.
Kindly guide us as soon as possible.
--
Regards,
Sharon D'Morris,
JRF
Amrita Center for Nanosciences and Molecular Medicine(ACNSMM)
Amrita Institute of Medical sciences,
AIMS-Ponekkara (P.O)
Kochi-682041
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Received on Wed Apr 25 2018 - 23:30:02 PDT
