Aunity
commented
6 days ago Please check your ligand's formal charge. And you can use the unigbsa-validate to fix this problem.
unigbsa-validate -i NADP.mol2 -o NADP.sdfPlease double check the output sdf file.
(gbsa) dell@dell-OptiPlex-Tower-Plus-7010:~/Videos/unigbsa_ZaHSD$ unigbsa-pipeline -i com_rep.pdb -l NADP.mol2 -c default2.ini -o OUTFILE -nt 30 --decomp --verbose 10/05/2024 17:31:35 PM - INFO - Build protein topology. 10/05/2024 17:31:36 PM - INFO - Build ligand topology: NADP. export OMP_NUM_THREADS=1;acpype -i /home/dell/Videos/unigbsa_ZaHSD/NADP./NADP..mol -b MOL -a gaff -c bcc -n 0 -k "grms_tol=0.005,qm_theory='AM1',scfconv=1.d-8,ndiis_attempts=700,maxcyc=0" -f >acpype.log 2>&1
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2023.10.27 (c) 2024 AWSdS |
==> ... charge set to 0 ==> Executing Antechamber... ERROR: ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ERROR: Welcome to antechamber 22.0: molecular input file processor.
Info: The atom type is set to gaff; the options available to the -at flag are gaff, gaff2, amber, bcc, and sybyl.
Info: Determining atomic numbers from atomic symbols which are case sensitive. Running: /home/dell/anaconda3/envs/gbsa/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac Info: Bond types are assigned for valence state (1) with penalty (1).
Running: /home/dell/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Info: Total number of electrons: 381; net charge: 0 Info: The number of electrons is odd (381). Please check the total charge (-nc flag) and spin multiplicity (-m flag).
Running: /home/dell/anaconda3/envs/gbsa/bin/sqm -O -i sqm.in -o sqm.out /home/dell/anaconda3/envs/gbsa/bin/wrapped_progs/antechamber: Fatal Error! Cannot properly run "/home/dell/anaconda3/envs/gbsa/bin/sqm -O -i sqm.in -o sqm.out".
ERROR: ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ERROR: Antechamber failed ERROR: ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ERROR: Cannot open file (MOL_bcc_gaff.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: 'MOL_AC.prmtop' Traceback (most recent call last): File "/home/dell/anaconda3/envs/gbsa/lib/python3.12/site-packages/acpype/cli.py", line 138, in init_main molecule.createMolTopol() File "/home/dell/anaconda3/envs/gbsa/lib/python3.12/site-packages/acpype/topol.py", line 1115, in createMolTopol self.topFileData = open(self.acTopFileName).readlines() ^^^^^^^^^^^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: 'MOL_AC.prmtop' Total time of execution: less than a second Traceback (most recent call last): File "/home/dell/anaconda3/envs/gbsa/lib/python3.12/site-packages/unigbsa/pipeline.py", line 139, in single build_topol(receptor, ligandfile, outpdb=grofile, outtop=topfile, File "/home/dell/anaconda3/envs/gbsa/lib/python3.12/site-packages/unigbsa/simulation/topology.py", line 219, in build_topol moltop, molgro = build_lignad(ligand, forcefield=ligandforce, charge_method=charge_method, nt=nt, verbose=verbose) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/dell/anaconda3/envs/gbsa/lib/python3.12/site-packages/unigbsa/simulation/topology.py", line 68, in build_lignad raise Exception('ERROR run the acpype. see the %s for details.'%os.path.abspath("acpype.log")) Exception: ERROR run the acpype. see the /home/dell/Videos/unigbsa_ZaHSD/NADP./NADP..TOP/acpype.log for details. 10/05/2024 17:31:36 PM - WARNING - Failed to generate forcefield for ligand: NADP. NADP.zip