Open entropybit opened 7 months ago
Hello!
I believe this is very related to the issue raised in https://github.com/choderalab/espaloma/issues/209, basically you would need to reparameterize the protein with something similar to what the following script is using, https://github.com/choderalab/vanilla-espaloma-experiment/blob/main/experiment/script/create_system.py (please note that it requires OpenEye).
Something that uses RDkit instead of openeye should be possible to do, but we don't have any script or tool for that.
There have been a series of questions regarding this, we definitely need to make this easier for users, but so far this is what we can offer. Thanks for your interest and I hope this helps!
Hi,
this might be a naive question and also somewhat of a function of my inexperience, but: I cant figure out how to load a ligand from a MOL file and than combine it with a PDB for the protein so that I get a complex which is parametrized using espaloma. As far as I understood the paper correct, the model can giver parameters for small molecules as well as proteins so this should be possible right ? Sorry for my possibly very uninformed question and thanks in advance for your answer.
To make this a bit more specific what I have tried is something like this:
Based on the PDB 4GIH which I preprocessed with pdbfixer. With this code I get the following error
So far what ever I tried I get an No template found for residue error with either the small molecule or one of the amino acids. Help would be appreciated ^^