molfile_to_params.py

[Anonymous]

Hi all,

I’m trying to run the molfile_to_params.py script.

I run into an import error: “No module named rosetta_py.io.mdl_molfile”

Anyone know where I can find and download rosetta_py for pyrosetta?

I can’t seem to find it online…

 

Thank you

[Anonymous]

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).

[Anonymous]

Got it to work! Thank you!

[Anonymous]

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.

[Anonymous]

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

[Anonymous]

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!

[Author]

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