[phenixbb] phenix.elbow: Best ploy to generate restraints files for similar compounds ?
pjeffrey at princeton.edu
Thu Apr 25 13:01:09 PDT 2013
I've got homologues of small molecule compounds I want to generate
restraints for. The changes I'm looking at are converting O to S and
moving a substituent around on a phenyl ring. I expect them to have
similar conformations overall.
Is the best method to:
1. create a new PDB file of the homolog, change atom types and do some
primitive modeling, assuming that the --opt method will fix geometry snafus
2. use a SMILES string, edit the numbering of the PDB file and
regenerate the restraints from that
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