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ccsb-scripps / AutoDock-Vina

AutoDock Vina
http://vina.scripps.edu
Apache License 2.0
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documentation fixes #150

Closed rczerminski-valo closed 1 year ago

rczerminski-valo commented 1 year ago
  1. added -U nphs_lps_waters option for prepare_receptor to prevent Zn removal
  2. note to explain situation when no TZ atoms are added
diogomart commented 1 year ago

Thank you @rczerminski-valo

Looks like prepare_receptor removes chains if all residues in that chain are non standard. In example/docking_with_zinc_metalloproteins/data/proteinH.pdb the zinc is in the same chain as the protein residues of the protein, which are standard residues, so zinc was not removed. Now, if zinc is the only residue in its own chain, it is removed. I'll add this info and merge. Thanks again.