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Hi RoseTTAFold-All-Atom team!
I am having an issue with a small molecule I want to dock into my protein. Given the molecule is a bit complex (contains Fe and Si), I want to opt out of openbabel generating conformers using the default (or any) forcefield. I thought I disabled this feature by making the relevant changes in small_molecule.py and parsers.py:
I am however still seeing a different structure that I submitted with my sdf file. Is there some other relaxation of the small_molecule that I'm missing?If this is part of the docking algorithm, can you point me in the right direction for troubleshooting?
The text was updated successfully, but these errors were encountered:
Hi RoseTTAFold-All-Atom team!
I am having an issue with a small molecule I want to dock into my protein. Given the molecule is a bit complex (contains Fe and Si), I want to opt out of openbabel generating conformers using the default (or any) forcefield. I thought I disabled this feature by making the relevant changes in small_molecule.py and parsers.py:
def parse_mol(filename, filetype="mol2", string=False, remove_H=False, find_automorphs=False, generate_conformer: bool = False):
in parsers.py
and
in small_molecules.py
I am however still seeing a different structure that I submitted with my sdf file. Is there some other relaxation of the small_molecule that I'm missing?If this is part of the docking algorithm, can you point me in the right direction for troubleshooting?
The text was updated successfully, but these errors were encountered: