[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>
    app.loadcheck_prmtops()
  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
    inst.initialize_topology()
  File "/opt/amber14/lib/python2.6/site-packages/chemistry/amber/_amberparm.py", line 196, in initialize_topology
    self.load_structure()
  File "/opt/amber14/lib/python2.6/site-packages/chemistry/amber/_amberparm.py", line 390, in load_structure
    self._load_extra_exclusions()
  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
12/20/2016
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Received on Tue Dec 20 2016 - 06:30:02 PST
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