Hello,
Upon running MMGBSA for protein-ligand complex with Mn2+ ions present
the script fails yielding:
```
Loading and checking parameter files for compatibility...
cpptraj found! Using /opt/apps/amber20/bin/cpptraj
sander found! Using /opt/apps/amber20/bin/sander
Preparing trajectories for simulation...
3001 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /opt/apps/amber20/bin/sander
calculating complex contribution...
bad atom type: Mn
File "/opt/apps/amber20/bin/MMPBSA.py", line 100, in <module>
app.run_mmpbsa()
File
"/opt/apps/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/opt/apps/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/opt/apps/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
line 156, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /opt/apps/amber20/bin/sander failed with prmtop
../parms/com.parm7!
Exiting. All files have been retained.
```
I checked ParmEd, all data necessary for calculations seems correct:
```
> printDetails :350
The mask :350 matches 1 atoms:
ATOM RES RESNAME NAME TYPE At.# LJ Radius LJ Depth
Mass Charge GB Radius GB Screen
5669 350 MN MN Mn2+ 25 1.4010 0.0159
54.9400 2.0000 1.5000 0.8000
```
What can I do to calculate relative binding energy? For simulation
itself, I used ff19SB+OPC+GAFF2.
Regards,
Rafał
--
dr inż. Rafał Madaj
Laboratorium Bioinformatyki Strukturalnej
Instytut Biologii Ewolucyjnej
Wydział Biologii UW
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Received on Tue Oct 04 2022 - 03:30:02 PDT
