molfile_to_params.py

The molfile_to_params.py script relies on some utility packages which can be found in the same directory the molfile_to_params.py script is located. It should be set up such that if you run the molfile_to_params.py script from the original directory, things should work. (Your working directory doesn’t need to be the original directory, but the molfile_to_params.py script should be located there.) If you move the molfile_to_params.py script to a different location, you’ll also have to move the associated package directories with it.

The rosetta_py package can’t be found elsewhere online, as it’s not really something that is installed separately from molfile_to_params.py — it’s something which is just kept in the same directory as the molfile_to_params.py script (and not “installed” per se).

Hi all,

I am running molfile_to_params.py for my ligand to get the .params file, but the .params file generated by this script is not matched with .mol2 file that I use. This script changes the name of atoms and gives me a new pdb file in which name of atoms are different from my original .mol2 file. Moreover, I get a warning when running this code. I am attaching the screenshot.

It is noteworthy to mention that all atom names in my ligand are unique.

P.M: my original pdb file is mySPT.pdb and the pdb file generated by the code is FRM_0001.pdb

I would be grateful,if you could help me.

Hi again,

I have another question: I have a ligand which is composed of protein+lipid and it is a big molecule. How can we use molfile_to_params.py and get a .params file? i tried it once, but it gave me several .params and several pdb files as output.

Can you help me with that?

Thank you

Can any of you attach the .txt file of the molfile_to_params.py file because I’m having a problem and I believe it’s because something’s lacking from my script. The read_mdl_sdf function is not defined. So I can’t turn any file into params. If you can I would be very thankful.

Thank you!