Dear Team pmx
I was trying to follow the tutorial from pmx given in the following link:
http://pmx.mpibpc.mpg.de/Old_Tutorials/janssen_tutorial_ligand/index.html
The process followed:
The lig_1a and lig_5 were downloaded from the above page, unzipped and kept in a folder. Then:
- The first step is to merge both ffMOL.itp files into one. I was able to run the script one_ff_file.py using the following command.
python one_ff_file.py -ffitp lig_1a/ffMOL.itp lig_5/ffMOL.itp -ffitp_out ffMOL.itp
Running the above command successfully generated ffMOL.itp - The second step, atom mapping has to be done using the script atoms_to_morph.py using the following command.
python atoms_to_morph.py -i1 lig_1a/lig_1a.pdb -i2 lig_5/lig_5.pdb -o pairs.dat - alignment -H2H
The above step was done by activating the pmx environment as indicated by the instructions. . Initially there were some some warning on indentation errors. Cleared those issues, and I was able to run the script without error/warning.
Now the problem is I was unable to find the output files in the working folder. How to resolve it? I observe that in def main() in script atom_to_morph.py there is no commands invoked. Please let me know if I have to tweak this.
Thanks, and regards