[AMBER] bad atom type MN2+ ions in the binding free energy decomposition (Amber14)

From: Ԭ <0444909yuan.163.com>
Date: Tue, 20 Dec 2016 22:25:27 +0800 (CST)

Hi everybody,
I've got a complex system including protein, RNA, two MN2+ ions and the drug to simulate in Amber14.
After I downloaded the parameter of the ions and loaded, the simulation and the binding free energy calculation (MM/GBSA and MM/PBSA) were completed successfully.
However, the binding free energy decomposition was failed by either GB or PB method in mm_pbsa.pl.
The error information for GB was "Bad Atom Type MN".
The error information for PB was more complicated:
"No values for GB_SGBSUR existing -> Skipping" "No values for PB_TPBSOL existing -> Skipping" "No values for PB_BPBSOL existing -> Skipping"
And these errors came one by one, like a wrong endless loop. I have to manually interrupt the process.
I have tried solutions found in the archives of Amber mailing list, including modifying the files of mdread2.F90 and mm_pbsa_calceneent.pm and recompiled the software. But the errors came as before.
I have also tried MM_PBSA.py. But error message appeared immediately:
Loading and checking parameter files for compatibility...
  File "/opt/amber14/bin/MMPBSA.py", line 102, in <module>
  File "/opt/amber14/lib/python2.6/site-packages/MMPBSA_mods/main.py", line 572, in loadcheck_prmtops
    FILES.receptor_prmtop, FILES.ligand_prmtop)
  File "/opt/amber14/lib/python2.6/site-packages/MMPBSA_mods/parm_setup.py", line 98, in __init__
    self.complex_prmtop = LoadParm(complex_prmtop)
  File "/opt/amber14/lib/python2.6/site-packages/chemistry/amber/readparm.py", line 69, in LoadParm
    parm = parm.view(AmberParm)
  File "/opt/amber14/lib/python2.6/site-packages/chemistry/amber/amberformat.py", line 411, in view
    return cls.load_from_rawdata(self)
  File "/opt/amber14/lib/python2.6/site-packages/chemistry/amber/_amberparm.py", line 240, in load_from_rawdata
  File "/opt/amber14/lib/python2.6/site-packages/chemistry/amber/_amberparm.py", line 196, in initialize_topology
  File "/opt/amber14/lib/python2.6/site-packages/chemistry/amber/_amberparm.py", line 390, in load_structure
  File "/opt/amber14/lib/python2.6/site-packages/chemistry/amber/_amberparm.py", line 1323, in _load_extra_exclusions
    real_atom = atom.bond_partners[0]
IndexError: list index out of range
Exiting. All files have been retained.

Thank you very much for any of your suggestions, advice and solutions.

Best regards,
HL Yuan
AMBER mailing list
Received on Tue Dec 20 2016 - 06:30:02 PST
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