Can I supply a ligand coordinate file as input?

protocaller / ProtoCaller

Full automation of relative protein-ligand binding free energy calculations in GROMACS

http://protocaller.readthedocs.io

GNU General Public License v3.0

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Can I supply a ligand coordinate file as input? #28

Closed xiki-tempula closed 3 years ago

xiki-tempula commented 3 years ago

Sorry, I'm new to ProtoCaller. I wodner if it is possible to feed pdb instead of smiles string as ligand input? Like ProtoCaller.Ensemble.Ligand.Ligand('lig.pdb')

tsenapathi commented 3 years ago

Hi @xiki-tempula you can use the coordinates of ligands as an SDF file. See the Sialyltransferase example https://github.com/protocaller/ProtoCaller/blob/master/examples/Sialyltransferase_2.py