Dear Pymol users,
I've decide to make a copy of this topic from the amber mail list because
this problem could be solves by ones of the methods implemented in Pymol.
Here I'm facing with the problem of the preparation of protein-ligand
complexes for amber md simulation:
Following amber's tutorial I've made parametrization of the ligand using
antechamber obtaining ligand.frcmod and ligand.lib files consisted of the
parameters for my ligand and its coordinates in mol2 associated with those
topologies. Now I'd like to dock this ligand to the active site of the
receptor using autodock vina and make further tleap processing of
complex.pdb produced by autodock to obtain all input data for simulation.
Here some problems: because (superimposed to the receptor cavity)
ligand.pdb produced by autodock have been stripped from all hydrogen’s so
its coordinates not equal to initial ligand.mol2 . How do you think will it
possible to use some method of the ligand superimposition to superimpose
initial ligand.mol2 (with correct corrdinates) agains docking pose produced
by vina and use superimposed ligand.mol2 for the preparation of my complex?
Thanks for help,
James
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