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dptech-corp / Uni-GBSA

An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculation.
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Running errors #48

Open Tangbbmc opened 6 months ago

Tangbbmc commented 6 months ago

When I run uni-GBSA using unigbsa-pipline in a batch mode, the following errors occurred. And, the partial results for some ligands did not have energy values (such as B00734_out,1,gb,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,F_top DB01184_out)

3/10/2024 21:20:44 PM - INFO - Build protein topology. 0%| | 0/37 [00:00<?, ?it/s]export OMP_NUM_THREADS=1;acpype -i /home/dell/Documents/NgIDH_VS/2a_DrugRep/37mol/DB00222_out.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 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).

Running: /home/dell/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Info: Total number of electrons: 231; net charge: 0 Info: The number of electrons is odd (231). 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 export OMP_NUM_THREADS=1;acpype -i /home/dell/Documents/NgHSD_VS/2a_DrugRep/37mol/DB00398_out.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 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).

Running: /home/dell/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Info: Total number of electrons: 225; net charge: 0 Info: The number of electrons is odd (225). 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 export OMP_NUM_THREADS=1;acpype -i /home/dell/Documents/NgHSD_VS/2a_DrugRep/37mol/DB00563_out.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 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).

Running: /home/dell/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Info: Total number of electrons: 223; net charge: 0 Info: The number of electrons is odd (223). 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 export OMP_NUM_THREADS=1;acpype -i /home/dell/Documents/NgHSD_VS/2a_DrugRep/37mol/DB00590_out.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 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).

Running: /home/dell/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Info: Total number of electrons: 215; net charge: 0 Info: The number of electrons is odd (215). 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 export OMP_NUM_THREADS=1;acpype -i /home/dell/Documents/NgHSD_VS/2a_DrugRep/37mol/DB00619_out.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 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).

Running: /home/dell/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Info: Total number of electrons: 233; net charge: 0 Info: The number of electrons is odd (233). 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 export OMP_NUM_THREADS=1;acpype -i /home/dell/Documents/NgHSD_VS/2a_DrugRep/37mol/DB00734_out.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 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).

Running: /home/dell/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Info: Total number of electrons: 191; net charge: 0 Info: The number of electrons is odd (191). 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 export OMP_NUM_THREADS=1;acpype -i /home/dell/Documents/NgHSD_VS/2a_DrugRep/37mol/DB01251_out.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 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).

Running: /home/dell/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Info: Total number of electrons: 249; net charge: 0 Info: The number of electrons is odd (249). 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 export OMP_NUM_THREADS=1;acpype -i /home/dell/Documents/NgHSD_VS/2a_DrugRep/37mol/DB01396_out.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 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).

Running: /home/dell/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Info: Total number of electrons: 355; net charge: 0 Info: The number of electrons is odd (355). 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 export OMP_NUM_THREADS=1;acpype -i /home/dell/Documents/NgHSD_VS/2a_DrugRep/37mol/DB00511_out.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 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).

Running: /home/dell/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Info: Total number of electrons: 374; net charge: 0

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: 7s export OMP_NUM_THREADS=1;acpype -i /home/dell/Documents/NgHSD_VS/2a_DrugRep/37mol/DB06144_out.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 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).

Running: /home/dell/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Info: Total number of electrons: 207; net charge: 0 Info: The number of electrons is odd (207). 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 03/10/2024 21:21:03 PM - INFO - Run the MMPB(GB)SA. export OMP_NUM_THREADS=1;acpype -i /home/dell/Documents/NgHSD_VS/2a_DrugRep/37mol/DB09078_out.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 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).

Running: /home/dell/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Info: Total number of electrons: 207; net charge: 0 Info: The number of electrons is odd (207). 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 03/10/2024 21:21:04 PM - INFO - Run the MMPB(GB)SA. export OMP_NUM_THREADS=1;acpype -i /home/dell/Documents/NgHSD_VS/2a_DrugRep/37mol/DB09079_out.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 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).

Running: /home/dell/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Info: Total number of electrons: 255; net charge: 0 Info: The number of electrons is odd (255). 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 03/10/2024 21:21:07 PM - INFO - Run the MMPB(GB)SA. export OMP_NUM_THREADS=1;acpype -i /home/dell/Documents/NgHSD_VS/2a_DrugRep/37mol/DB11256_out.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 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).

Running: /home/dell/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Info: Total number of electrons: 225; net charge: 0 Info: The number of electrons is odd (225). 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 03/10/2024 21:21:11 PM - INFO - Run the MMPB(GB)SA. 03/10/2024 21:21:12 PM - INFO - Run the MMPB(GB)SA. export OMP_NUM_THREADS=1;acpype -i /home/dell/Documents/NgHSD_VS/2a_DrugRep/37mol/DB11581_out.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 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).

Running: /home/dell/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Info: Total number of electrons: 411; net charge: 0 Info: The number of electrons is odd (411). 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 export OMP_NUM_THREADS=1;acpype -i /home/dell/Documents/NgHSD_VS/2a_DrugRep/37mol/DB11596_out.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 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).

Running: /home/dell/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Info: Total number of electrons: 233; net charge: 0 Info: The number of electrons is odd (233). 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 03/10/2024 21:21:13 PM - INFO - Run the MMPB(GB)SA. 03/10/2024 21:21:13 PM - INFO - Run the MMPB(GB)SA. export OMP_NUM_THREADS=1;acpype -i /home/dell/Documents/NgHSD_VS/2a_DrugRep/37mol/DB11732_out.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 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).

Running: /home/dell/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Info: Total number of electrons: 179; net charge: 0 Info: The number of electrons is odd (179). 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 export OMP_NUM_THREADS=1;acpype -i /home/dell/Documents/NgHSD_VS/2a_DrugRep/37mol/DB12978_out.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 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).

Running: /home/dell/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Info: Total number of electrons: 201; net charge: 0 Info: The number of electrons is odd (201). 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 03/10/2024 21:21:21 PM - INFO - Run the MMPB(GB)SA. 03/10/2024 21:21:22 PM - INFO - Run the MMPB(GB)SA. 03/10/2024 21:21:22 PM - INFO - Run the MMPB(GB)SA. 03/10/2024 21:21:23 PM - INFO - Run the MMPB(GB)SA. 03/10/2024 21:21:23 PM - INFO - Run the MMPB(GB)SA. 03/10/2024 21:21:27 PM - INFO - Run the MMPB(GB)SA. 03/10/2024 21:21:31 PM - INFO - Run the MMPB(GB)SA. 03/10/2024 21:21:32 PM - INFO - Run the MMPB(GB)SA. 03/10/2024 21:21:36 PM - INFO - Run the MMPB(GB)SA. 03/10/2024 21:21:37 PM - INFO - Run the MMPB(GB)SA. 03/10/2024 21:21:38 PM - INFO - Run the MMPB(GB)SA. 03/10/2024 21:21:40 PM - INFO - Run the MMPB(GB)SA. 03/10/2024 21:22:07 PM - INFO - Run the MMPB(GB)SA. 03/10/2024 21:23:00 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -50.4484
03/10/2024 21:23:03 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -53.8445
03/10/2024 21:23:05 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -44.0138
3%|█ | 1/37 [02:17<1:22:19, 137.21s/it]03/10/2024 21:23:08 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -42.8089
03/10/2024 21:23:10 PM - INFO - Clean the results. 03/10/2024 21:23:10 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -47.3233

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -45.4563
8%|███▌ | 3/37 [02:22<21:16, 37.54s/it]03/10/2024 21:23:16 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -50.4495
03/10/2024 21:23:17 PM - INFO - Clean the results. 03/10/2024 21:23:17 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -46.7604

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -46.0066
03/10/2024 21:23:18 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -46.7059
03/10/2024 21:23:19 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -48.0356
11%|████▊ | 4/37 [02:31<15:15, 27.75s/it]03/10/2024 21:23:20 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -54.4227
03/10/2024 21:23:24 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -50.6699
49%|████████████████████▉ | 18/37 [02:36<01:12, 3.80s/it]03/10/2024 21:23:27 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -38.8843
03/10/2024 21:23:30 PM - INFO - Clean the results. 03/10/2024 21:23:30 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -50.5240

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -45.4994
03/10/2024 21:23:32 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -54.2276
51%|██████████████████████ | 19/37 [02:44<01:14, 4.13s/it]03/10/2024 21:23:35 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -41.1716
70%|██████████████████████████████▏ | 26/37 [02:46<00:26, 2.43s/it]03/10/2024 21:23:36 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -50.1121
03/10/2024 21:23:38 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv Frames mode detal_G(kcal/mole) 1 gb -39.9678

Aunity commented 6 months ago

Could you upload your input files? It seems your ligands have some problems.

Tangbbmc commented 6 months ago

@Aunity > Could you upload your input files? It seems your ligands have some problems. Ok. I have uploaded partial ligand files. Please help me to check them! Thank you! I am looking forward to your reply as soon as possible!

Ligands_error.zip

Aunity commented 6 months ago

Your ligand files need to add hydrogens before run the unigbsa. And you can use the command of unigbsa-validate to check and repair your ligand files.

Tangbbmc commented 6 months ago

Ok.Thank you very much for your kind help!

---- Replied Message ---- From Maohua @.> Date 03/14/2024 14:54 To @.> Cc @.>@.> Subject Re: [dptech-corp/Uni-GBSA] Running errors (Issue #48)

Your ligand files need to add hydrogens before run the unigbsa. And you can use the command of unigbsa-validate to check and repair your ligand files. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>