This is a very good job, but I encountered the following error while running the first example：
$ unigbsa-pipeline -i example/1ceb/1ceb_protein.pdb -l example/1ceb/1ceb_ligand.sdf -o BindingEnergy.csv
The following is the error message：

01/18/2024 21:29:59 PM - INFO - Build protein topology.

01/18/2024 21:30:00 PM - INFO - Build ligand topology: 1ceb_ligand
01/18/2024 21:30:04 PM - INFO - Running energy minimization: 1ceb_ligand
sh: line 1: 19327 Segmentation fault gmx mdrun -v -deffnm minim -nt 1 -ntmpi 1 >> gromacs.log 2>&1
gmx mdrun -v -deffnm minim -nt 1 -ntmpi 1
Generating 1-4 interactions: fudge = 0.5
Number of degrees of freedom in T-Coupling group rest is 4479.00
The integrator does not provide a ensemble temperature, there is no system ensemble temperature

NOTE 2 [file /home/panfulu/anaconda3/envs/uni/lib/python3.8/site-packages/unigbsa/simulation/mdp/minim.mdp]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance, increase the cut-off and the PME grid spacing.

There were 2 NOTEs

Back Off! I just backed up minim.tpr to ./#minim.tpr.1#

GROMACS reminds you: "Ubiquitin's just a rock" (Berk Hess)

Setting the LD random seed to -697645185

Generated 741 of the 741 non-bonded parameter combinations

Generated 741 of the 741 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type 'MOL'

Excluding 3 bonded neighbours molecule type 'system1'

Excluding 3 bonded neighbours molecule type 'SOL'
Analysing residue names:
There are: 1 Other residues
There are: 80 Protein residues
There are: 81 Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing Protein...

The largest distance between excluded atoms is 0.491 nm between atom 1244 and 1251
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 52x42x40, spacing 0.112 0.118 0.110

Estimate for the relative computational load of the PME mesh part: 0.68

This run will generate roughly 0 Mb of data
:-) GROMACS - gmx mdrun, 2023.1-conda_forge (-:

Executable: /home/panfulu/anaconda3/envs/uni/bin.AVX2_256/gmx
Data prefix: /home/panfulu/anaconda3/envs/uni
Working dir: /home/panfulu/project/Uni-GBSA/1ceb_ligand/complex.GMX
Command line:
gmx mdrun -v -deffnm minim -nt 1 -ntmpi 1

Traceback (most recent call last):
File "/home/panfulu/anaconda3/envs/uni/lib/python3.8/site-packages/unigbsa/pipeline.py", line 149, in single
minimgro, outtop = engine.run_to_minim(grofile, topfile,
File "/home/panfulu/anaconda3/envs/uni/lib/python3.8/site-packages/unigbsa/simulation/mdrun.py", line 385, in run_to_minim
minipdb = self.gmx_minim(ionspdb, topfile, mdpfile=os.path.join(MDPFILESDIR, 'minim.mdp'), nt=nt)
File "/home/panfulu/anaconda3/envs/uni/lib/python3.8/site-packages/unigbsa/simulation/mdrun.py", line 200, in gmx_minim
outfile = self._mdrun(outtpr, nt)
File "/home/panfulu/anaconda3/envs/uni/lib/python3.8/site-packages/unigbsa/simulation/mdrun.py", line 80, in _mdrun
raise Exception('ERROR run mdrun %s. See the logfile for details %s'%(tprfile, os.path.abspath(self.gmxlog)))
Exception: ERROR run mdrun minim.tpr. See the logfile for details /home/panfulu/project/Uni-GBSA/1ceb_ligand/complex.GMX/gromacs.log
01/18/2024 21:30:06 PM - WARNING - Failed to run simulation for ligand: 1ceb_ligand

The following is the information in the gromacs.log file:

           :-) GROMACS - gmx editconf, 2023.1-conda_forge (-:

Executable: /home/panfulu/anaconda3/envs/uni/bin.AVX2_256/gmx
Data prefix: /home/panfulu/anaconda3/envs/uni
Working dir: /home/panfulu/project/Uni-GBSA/1ceb_ligand/complex.GMX
Command line:
gmx editconf -f /home/panfulu/project/Uni-GBSA/1ceb_ligand/complex.pdb -o box.pdb -bt triclinic -d 0.900000

Back Off! I just backed up box.pdb to ./#box.pdb.1#

GROMACS reminds you: "Ubiquitin's just a rock" (Berk Hess)

Note that major changes are planned in future for editconf, to improve usability and utility.
Read 1494 atoms
Volume: 1272.11 nm^3, corresponds to roughly 572400 electrons
No velocities found
system size : 3.999 3.165 2.596 (nm)
center : 1.793 -0.188 3.244 (nm)
box vectors : 13.956 11.878 7.674 (nm)
box angles : 90.00 90.00 90.00 (degrees)
box volume :1272.11 (nm^3)
shift : 1.106 2.670 -1.046 (nm)
new center : 2.900 2.482 2.198 (nm)
new box vectors : 5.799 4.965 4.396 (nm)
new box angles : 90.00 90.00 90.00 (degrees)
new box volume : 126.57 (nm^3)
:-) GROMACS - gmx grompp, 2023.1-conda_forge (-:

Executable: /home/panfulu/anaconda3/envs/uni/bin.AVX2_256/gmx
Data prefix: /home/panfulu/anaconda3/envs/uni
Working dir: /home/panfulu/project/Uni-GBSA/1ceb_ligand/complex.GMX
Command line:
gmx grompp -f /home/panfulu/anaconda3/envs/uni/lib/python3.8/site-packages/unigbsa/simulation/mdp/minim.mdp -c /home/panfulu/project/Uni-GBSA/1ceb_ligand/complex.GMX/box.pdb -r /home/panfulu/project/Uni-GBSA/1ceb_ligand/complex.GMX/box.pdb -o minim.tpr -p /home/panfulu/project/Uni-GBSA/1ceb_ligand/complex.GMX/complex.top -maxwarn 5

Ignoring obsolete mdp entry 'ns_type'

NOTE 1 [file /home/panfulu/anaconda3/envs/uni/lib/python3.8/site-packages/unigbsa/simulation/mdp/minim.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.

Generating 1-4 interactions: fudge = 0.5
Number of degrees of freedom in T-Coupling group rest is 4479.00
The integrator does not provide a ensemble temperature, there is no system ensemble temperature

NOTE 2 [file /home/panfulu/anaconda3/envs/uni/lib/python3.8/site-packages/unigbsa/simulation/mdp/minim.mdp]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance, increase the cut-off and the PME grid spacing.

There were 2 NOTEs

Back Off! I just backed up minim.tpr to ./#minim.tpr.1#

GROMACS reminds you: "Ubiquitin's just a rock" (Berk Hess)

Setting the LD random seed to -697645185

Generated 741 of the 741 non-bonded parameter combinations

Generated 741 of the 741 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type 'MOL'

Excluding 3 bonded neighbours molecule type 'system1'

Excluding 3 bonded neighbours molecule type 'SOL'
Analysing residue names:
There are: 1 Other residues
There are: 80 Protein residues
There are: 81 Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing Protein...

The largest distance between excluded atoms is 0.491 nm between atom 1244 and 1251
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 52x42x40, spacing 0.112 0.118 0.110

Estimate for the relative computational load of the PME mesh part: 0.68

This run will generate roughly 0 Mb of data
:-) GROMACS - gmx mdrun, 2023.1-conda_forge (-:

Executable: /home/panfulu/anaconda3/envs/uni/bin.AVX2_256/gmx
Data prefix: /home/panfulu/anaconda3/envs/uni
Working dir: /home/panfulu/project/Uni-GBSA/1ceb_ligand/complex.GMX
Command line:
gmx mdrun -v -deffnm minim -nt 1 -ntmpi 1

Dear authors,

Very nice tool!

I want to ask for some help.

After running the unigbsa-md command, I got the "1ceb_ligand.mol", "complex.gro", "complex.pdb", "complex.top", and "traj_comx.xtc" files.

And I want to run the unigbsa-traj command, however, it needs to prepare a gromacs index.ndx file which contains two groups named RECEPTOR and LIGAND. Although I refer to https://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html, it is still not clear.

Could you specify the command of how to prepare this file?

Thank you very much!

The receptor contains a calcium ion located at its active center. I want to calculate the free energy of a ligand targeting the active center of receptor on the receptor. Can uni-GBSA perform this calculation? Thank you!

I want to fix the seed when running pipeline and md (because the result value changes every time I execute the same command).
However, there is no command option to control the seed, and the implementation is so complicated that I don't know how to specify the seed.

Hi,

The tool seems to require a pre-compiled gromacs (gmx) to work from the container. Is it possible to provide the absolute path of an external gromacs container (as a docker or a singularity image) as a command line argument such that it can use it instead of looking locally for an installed gmx binaries,

Thanks

Hello, thanks a lot for sharing your work!

I wanted to ask whether it is possible to use GPU for short MD simulations, as I did not notice any options of specifying the device.

Thanks!

unigbsa-traj -i example/3f/complex.pdb -p example/3f/complex.top -ndx example/3f/index.ndx -m pb gb -t example/3f/complex.pdb
12/24/2022 19:42:10 PM - INFO - Run the MMPB(GB)SA.
12/24/2022 19:45:18 PM - INFO - Clean the results.

Results: Energy.csv Dec.csv
mode detal_G(kcal/mole) Std. Dev.
Frames 1.0000 1.0000
Traceback (most recent call last):
File "/home/phzd/miniconda3/envs/gbsa/bin/unigbsa-traj", line 33, in
sys.exit(load_entry_point('unigbsa==0.1.1', 'console_scripts', 'unigbsa-traj')())
File "/home/phzd/miniconda3/envs/gbsa/lib/python3.8/site-packages/unigbsa/CLI.py", line 272, in traj_pipeline
print('%4s %18.4f %9.4f'%(k, v[0], v[1]))
TypeError: must be real number, not str

in CLI.py line 269,
"""
pbsa.extract_result()
detal_G = pbsa.extract_result()
print("mode detal_G(kcal/mole) Std. Dev.")
for k, v in detal_G.items():
print('%4s %18.4f %9.4f'%(k, v[0], v[1]))
"""
detal_G is a str, the content was showed using pdb:
"""
Frames mode complex receptor ... Non-Polar Solvation Gas Solvation TOTAL
0 1 gb -18064.469231 -17974.039669 ... -7.127718 -73.4565 20.576882 -52.879618
1 1 pb -16442.770400 -16401.441600 ... 24.980200 -73.4565 70.751100 -2.705400
"""
same as file "Eenergy.csv"

I think the function "extract_result()" under class GBSA(object) in "gbsarun.py" file might need some modification

Hello, I'm just testing this package out and it appears very appealing for the purpose of running quick simulations in order to get a rough idea.
I'm now working on a system in which I have the receptor, a cofactor and a ligand.
Is it possible to run the simulation with both the cofactor and the ligand modeled using the gaff2 FF automatically through this package?

Hello,
I am using Uni-GBSA as:

unigbsa-pipeline -i receptor.pdb -l ligand.pdb -o outpud.csv -nt 10

but it only runs on a single CPU. How can I run the command in parallel on multiple CPUs?

Thanks in advance.

I executed the command mentioned in the tutorial:
unigbsa-pipeline -i example/1ceb/1ceb_protein.pdb -l example/1ceb/1ceb_ligand.sdf -o BindingEnergy.csv
However, I got an error during the execution. The error message states:
WARNING - Failed to run simulation for ligand: 1ceb_ligand
Through the command line, I found that the error might be caused by CUDA:
CUDA_ERROR_INVALID_PTX: a PTX JIT compilation failed

I am using a PC equipped with 2 Quadro P4000 GPUs. I would appreciate your guidance on resolving this error.

Thank you for your help!

If I add '-dec' to decompose energy when using unigbsa-traj, the following error will be raised:

unigbsa-traj: error: unrecognized arguments: -dec

Could you fix this?

Thank you very much!

Hi,

It is really an excellent work. However, I have met some issues when running your code.

File "/nas-alinlp/lhuang/miniconda/envs/gbsa/lib/python3.10/shutil.py", line 729, in rmtree
    os.rmdir(path)
OSError: [Errno 39] Directory not empty: '/ligand_file_name/UNIGBSA'

Could you please tell me how to solve it?

Previously, I have installed Gromacs and gmx_MMPBSA on my Ubuntu system. Then, when I will install uni-GBSA by conda, what are the issues I need to be aware of?

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