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openmm / pdbfixer

PDBFixer fixes problems in PDB files
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[WIP] Improved method of selecting positions for added residues #198

Closed peastman closed 2 weeks ago

peastman commented 4 years ago

This is an attempt at fixing some of the problems in #145. After selecting initial positions for added residues, but before running the main energy minimization, it optimizes a coarse grained model that represents each residue as a single bead. This should reduce the chance of a new residue getting put right on top of an existing one.

jchodera commented 4 years ago

@peastman: Is this still in the works, or is it ready to merge?

peastman commented 4 years ago

No, the changes so far didn't solve the problem. I'm still trying to figure it out.