[phenixbb] Help with custom bond restraints syntax
Andrew T. Torelli
att29 at cornell.edu
Tue Sep 29 08:54:12 PDT 2009
Hi all,
I'm having what I believe is a simple problem defining custom bond
restraints between a side chain in my protein model and a ligand
(non-covalent bond). Here is a minimal form of my custom bond
definition file that suffers from the error:
refinement.geometry_restraints.edits {
Atom1 = chain F and resid 1 and name FE1
Atom2 = chain A and resid 69 and name SG
bond {
action = *add
atom_selection_1 = Atom1
atom_selection_2 = Atom2
distance_ideal = 2.35
sigma = 0.1
slack = None
}
}
I'm using phenix 1.4-153 and I get the following error:
ERROR: Unused parameter definitions:
refinement.geometry_restraints.edits.Atom1 (file
"/HOME/andrew/PHENIX_paramfiles/test.edits", line 5)
refinement.geometry_restraints.edits.Atom2 (file
"/HOME/andrew/PHENIX_paramfiles/test.edits", line 6)
I've checked through the online manual and I believe my syntax is
correct, but I'm not sure why my custom bond restraint is being
ignored.
A second question is: once I get the custom bond/angle restraints
correctly implemented, is there a better or more convenient place to
look and confirm that the restraints have been imposed other than the
.geo file phenix.refine outputs?
Thank you very much for your help,
-Andy
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