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Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
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[Bug-gmx_MMPBSA]: bad atom type: MN #326

Closed Valdes-Tresanco-MS closed 1 year ago

Valdes-Tresanco-MS commented 1 year ago

Bug summary

I'm trying to perform MM/GBSA calculations with decomposition analysis. My system is a metalloprotein (Mn2+) binding to an organic small ligand. When decomposition with GB is performed I get this error: bad atom type: MN

_Originally reported in https://groups.google.com/g/gmx_mmpbsa/c/YeTDAbXvurQ_

Terminal output

[INFO   ] Running calculations on normal system...
[INFO   ] Beginning GB calculations with /Users/GabrielaLima/Downloads/amber22/bin/sander
[INFO   ]   calculating complex contribution...
 bad atom type: MN
  File "/Users/GabrielaLima/opt/anaconda3/envs/gmx/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/Users/GabrielaLima/opt/anaconda3/envs/gmx/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 104, in gmxmmpbsa
    app.run_mmpbsa()
  File "/Users/GabrielaLima/opt/anaconda3/envs/gmx/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 203, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/Users/GabrielaLima/opt/anaconda3/envs/gmx/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 85, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/Users/GabrielaLima/opt/anaconda3/envs/gmx/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 161, in run
    raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /Users/GabrielaLima/Downloads/amber22/bin/sander failed with prmtop COM.prmtop!
Exiting. All files have been retained.

gmx_MMPBSA.log

N/A

Operating system

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gmx_MMPBSA Version

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Python version

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Installation

None

Valdes-Tresanco-MS commented 1 year ago

Unfortunately, this is a sander limitation. Solving it is complicated and requires basic programming knowledge. To include this atom, you must add to the radii definition list of the ICOSA method in sander (AmberTools22/src/sander/mdread2.F90, lines 1510-1572) this atom and then recompile the code. I am closing this issue because it is not directly related to gmx_MMPBSA, and there is nothing I can do to solve it.