alanwilter
commented
7 months ago Your PDB atom names do not seem to follow standard nomenclature:
---Judge bond type for Residue 2 with ID of 2 and Name of LO3 ---
/home/hicham/miniconda3/envs/gmx/bin/to_be_dispatched/antechamber: Fatal Error!
No Gasteiger parameter for atom (ID: 131, Name: H62, Type: DU). <------I also hope your system has only allowed atoms, check here
Hello, First thank for this useful package. secondly I was dealing with a ligand but I got this Error message: (gmx) hicham@DESKTOP-E3HV849:~/gmxNew/01-29$ acpype -i LO3.pdb
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2023.10.27 (c) 2024 AWSdS |
WARNING: no charge value given, trying to guess one... ERROR: guessCharge failed ERROR: ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ERROR: Welcome to antechamber 19.0: molecular input file processor.
---Judge bond type for Residue 1 with ID of 1 and Name of LO3 --- Warning: The assigned bond types may be wrong, please : (1) double check the structure (the connectivity) and/or (2) adjust atom valence penalty parameters in APS.DAT, and/or (3) increase PSCUTOFF in define.h and recompile bondtype.c (be cautious, using a large value of PSCUTOFF (>100) will significantly increase the computation time).
---Judge bond type for Residue 2 with ID of 2 and Name of LO3 --- /home/hicham/miniconda3/envs/gmx/bin/to_be_dispatched/antechamber: Fatal Error! No Gasteiger parameter for atom (ID: 131, Name: H62, Type: DU). ERROR: ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ==> Trying with net charge = 0 ... ==> ... charge set to 0 ==> ... converting pdb input file to mol2 input file ==> Babel OK ==> Executing Antechamber... ERROR: ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ERROR: Welcome to antechamber 19.0: molecular input file processor.
Info: Finished reading file (LO3.mol2); atoms read (134), bonds read (131). Running: /home/hicham/miniconda3/envs/gmx/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
---Judge bond type for Residue 1 with ID of 1 and Name of LO3 --- Warning: The assigned bond types may be wrong, please : (1) double check the structure (the connectivity) and/or (2) adjust atom valence penalty parameters in APS.DAT, and/or (3) increase PSCUTOFF in define.h and recompile bondtype.c (be cautious, using a large value of PSCUTOFF (>100) will significantly increase the computation time).
---Judge bond type for Residue 2 with ID of 2 and Name of LO3 ---
Running: /home/hicham/miniconda3/envs/gmx/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff2 Info: Total number of electrons: 512; net charge: 0
Running: /home/hicham/miniconda3/envs/gmx/bin/sqm -O -i sqm.in -o sqm.out Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG IEEE_DIVIDE_BY_ZERO IEEE_UNDERFLOW_FLAG IEEE_DENORMAL /home/hicham/miniconda3/envs/gmx/bin/to_be_dispatched/antechamber: Fatal Error! Unable to find sqm charges in file (sqm.out). Verify the filename and the file contents.
ERROR: ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ERROR: Antechamber failed ERROR: ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ERROR: Cannot open file (LO3_bcc_gaff2.mol2) with mode (r). No such file or directory ERROR: ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ERROR: Parmchk failed ERROR: Tleap failed ==> Removing temporary files... ERROR: ACPYPE FAILED: [Errno 2] No such file or directory: 'LO3_AC.prmtop' Traceback (most recent call last): File "/home/hicham/miniconda3/envs/gmx/lib/python3.8/site-packages/acpype/cli.py", line 138, in init_main molecule.createMolTopol() File "/home/hicham/miniconda3/envs/gmx/lib/python3.8/site-packages/acpype/topol.py", line 1115, in createMolTopol self.topFileData = open(self.acTopFileName).readlines() FileNotFoundError: [Errno 2] No such file or directory: 'LO3_AC.prmtop' Total time of execution: 17s