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choderalab / vanilla-espaloma-experiment

Vanilla MD simulation of protein-ligand complex using espaloma-0.3
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Molecule.from_file(protein_filename) #1

Open cuitaoyong opened 1 year ago

cuitaoyong commented 1 year ago

Molecule.from_file() can not read pdb file, what should I do? thank you

kntkb commented 1 year ago

Thank your for your interest. This might be related to our current work-around in loading PDB files into OpenFF Molecule objects. Currently, our script require the OpenEye toolkit to be installed which can be obtained for free for academics. More details can be found here.

cuitaoyong commented 1 year ago

Thank you for your answer. Is there any way to bypass OpenEye? The process of applying for OpenEye in my country is very complex, and I have been applying for it for a week, but there is still no news

ijpulidos commented 1 year ago

@cuitaoyong You could try to create the complex with something like what's discussed in https://docs.openforcefield.org/en/latest/examples/openforcefield/openff-toolkit/toolkit_showcase/toolkit_showcase.html which shouldn't require OpenEye. But you would need to adapt the scripts provided here for that to happen. Please consider that this approach has not been tested by us.

cuitaoyong commented 1 year ago

I also test codes only using openff without espaloma (using vanilla-espaloma-experiment-main/experiment/tyk2-lig_ejm_31/openff-2.1.0/prep/lsf-submit.sh). And I want to use " self. _simulation. reports. append(PDBReporter ('.. /vanilla espaloma experience main/output. pdb', 1))" to save all MD trajectories, but after the program runs, the pdb is still empty, making it difficult for me to determine if my code successfully ran MD, but there were no errors reported image

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cuitaoyong commented 1 year ago

@cuitaoyong You could try to create the complex with something like what's discussed in https://docs.openforcefield.org/en/latest/examples/openforcefield/openff-toolkit/toolkit_showcase/toolkit_showcase.html which shouldn't require OpenEye. But you would need to adapt the scripts provided here for that to happen. Please consider that this approach has not been tested by us.

Thanks! I will try it