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protocaller / ProtoCaller

Full automation of relative protein-ligand binding free energy calculations in GROMACS
http://protocaller.readthedocs.io
GNU General Public License v3.0
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error: unrecognized arguments: - q u i e t #11

Closed HCl0906 closed 4 years ago

HCl0906 commented 4 years ago

Hi, It's a useful tool. While I got some problem, and the following is details:

(base) [hcl@hcl-pc examples]$ python DHFR.py 

/home/hcl/miniconda3/lib/python3.7/site-packages/ProtoCaller/__init__.py:31: UserWarning: Cannot find MPI binary for the current operating system.
  _warnings.warn("Cannot find MPI binary for the current operating system.")
INFO:numexpr.utils:NumExpr defaulting to 4 threads.
INFO:root:Parametrising ligand Cl_H...
INFO:root:Running OpenBabel... 
INFO:root:Running antechamber... 
INFO:root:Running parmchk2... 
INFO:root:Running tleap... 
INFO:root:Parametrising ligand H_H...
INFO:root:Running OpenBabel... 
INFO:root:Running antechamber... 
INFO:root:Running parmchk2... 
INFO:root:Running tleap... 
INFO:root:Parametrising ligand OMe...
INFO:root:Running OpenBabel... 
INFO:root:Running antechamber... 
INFO:root:Running parmchk2... 
INFO:root:Running tleap... 
INFO:root:Parametrising ligand NO2...
INFO:root:Running OpenBabel... 
INFO:root:Running antechamber... 
INFO:root:Running parmchk2... 
INFO:root:Running tleap... 
INFO:root:Parametrising ligand Br...
INFO:root:Running OpenBabel... 
INFO:root:Running antechamber... 
INFO:root:Running parmchk2... 
INFO:root:Running tleap... 
INFO:root:Parametrising ligand Me_Me...
INFO:root:Running OpenBabel... 
INFO:root:Running antechamber... 
INFO:root:Running parmchk2... 
INFO:root:Running tleap... 
INFO:root:Parametrising ligand Me_H...
INFO:root:Running OpenBabel... 
INFO:root:Running antechamber... 
INFO:root:Running parmchk2... 
INFO:root:Running tleap... 
INFO:root:Parametrising ligand Cl_Cl...
INFO:root:Running OpenBabel... 
INFO:root:Running antechamber... 
INFO:root:Running parmchk2... 
INFO:root:Running tleap... 
Generating input files for 5HPB...
INFO:root:Downloading ligand files from the Protein Data Bank...
usage: DHFR.py [-h] [-f FILENAMES] [-r REFERENCE] [-c CHAINS]
               [-i TITRATE_ONLY] [-t THERMOPHILES] [-a ALIGNMENT]
               [-m MUTATIONS] [-v VERSION_LABEL] [-p PARAMETERS]
               [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-o PH]
               [-w WINDOW WINDOW WINDOW] [-g GRID GRID GRID]
               [--mutator MUTATOR] [--mutator-option MUTATOR_OPTIONS] [-d]
               [-l] [-k] [-q] [--generate-propka-input] [--protonate-all]
               input_pdb
DHFR.py: error: unrecognized arguments: - q u i e t
(base) [hcl@hcl-pc examples]$
msuruzhon commented 4 years ago

Hi there,

It seems that the PDB2PQR version we are using is not compatible with the most recent PROPKA version. Until this is fixed, I would suggest downgrading the PROPKA package:

conda install -c conda-forge propka=3.1.0

tsenapathi commented 4 years ago

Hello, @msuruzhon @HCl0906 I am working on fixing this issue. I will let you know about the updates here.

HCl0906 commented 4 years ago

Hi there,

It seems that the PDB2PQR version we are using is not compatible with the most recent PROPKA version. Until this is fixed, I would suggest downgrading the PROPKA package:

conda install -c conda-forge propka=3.1.0

Yeah it works, thanks!

HCl0906 commented 4 years ago

Hello, @msuruzhon @HCl0906 I am working on fixing this issue. I will let you know about the updates here.

Thanks!

tsenapathi commented 4 years ago

The pdb2pqr package is now updated in conda-forge to get the correct dependencies (https://anaconda.org/conda-forge/htmd-pdb2pqr). Apologies for my mistake forgot to change the dependency when I update PROPKA.

msuruzhon commented 4 years ago

Nice, I also updated the ProtoCaller dependencies just in case.

HCl0906 commented 4 years ago

Hi all, thanks a lot for your help! The issue has been solved.