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
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