search

TinkerTools / poltype2

Poltype 2: Automated Parameterization and Free Energy Prediction for AMOEBA
Other
41 stars 11 forks source link

Issue ldataparser #52

Closed TimotheMelin closed 3 months ago

TimotheMelin commented 3 months ago

The goal is to fix an issue when reading opbend prm fro mAMOEBA09.prm file

TimotheMelin commented 3 months ago

@leucinw we found an issue when parsing ameoba09.prm file for opbend prm. This is the issue from poltype:

Traceback (most recent call last):
  File "/usr/local/poltype/PoltypeModules/lDatabaseParser/lAssignAMOEBAplusPRM.py", line 1090, in <module>
    assignBonded(new_para, fitting)
  File "/usr/local/poltype/PoltypeModules/lDatabaseParser/lAssignAMOEBAplusPRM.py", line 790, in assignBonded
    assignOpbendA09(atom2class, key+"_bonded")
  File "/usr/local/poltype/PoltypeModules/lDatabaseParser/lAssignAMOEBAplusPRM.py", line 841, in assignOpbendA09
    current_v = float(s[-1])
ValueError: could not convert string to float: 'structure'
Fri Jul 26 22:21:16 2024 ERROR: python /usr/local/poltype/PoltypeModules/lDatabaseParser/lAssignAMOEBAplusPRM.py -xyz ligand.xyz_2 -key tmpbonded.key -sdf ligand.sdf -potent BONDED path = /mnt/Temp
Fri Jul 26 22:21:16 2024 Traceback (most recent call last):
  File "/usr/local/poltype/PoltypeModules/poltype.py", line 8200, in RunPoltype
    poltype.main()
  File "/usr/local/poltype/PoltypeModules/poltype.py", line 3649, in main
    params= self.GenerateParameters()
  File "/usr/local/poltype/PoltypeModules/poltype.py", line 4934, in GenerateParameters
    ldatabaseparser.assign_bonded_params(self)
  File "/usr/local/poltype/PoltypeModules/ldatabaseparser.py", line 292, in assign_bonded_params
    poltype.call_subsystem([cmd], True)
  File "/usr/local/poltype/PoltypeModules/poltype.py", line 3525, in call_subsystem
    raise ValueError("ERROR: " + cmdstr+' '+'path'+' = '+os.getcwd())
ValueError: ERROR: python /usr/local/poltype/PoltypeModules/lDatabaseParser/lAssignAMOEBAplusPRM.py -xyz ligand.xyz_2 -key tmpbonded.key -sdf ligand.sdf -potent BONDED path = /mnt/Temp

If you want to test, let me know I can give you the file to run lAssignAMOEBAplusPRM.py