[phenixbb] geometry minimization with ligand present
CPMAS Chen
cpmasmit at gmail.com
Wed Oct 19 19:04:09 PDT 2022
Hi, All,
I have a structure calculated with NMR restraints but it has quite some
geometry violation, such as torsion angles, clashes etc.
The structure has a small molecule ligand bound.
Is it possible to add an CIF file for the ligand and use
phenix.geometry_minimization to idealize/optimize the protein structure?
I have tried the following and phenix reported an error for missing CIF
file.
phenix.geometry_minimization model.pdb
pdb_intepretation.apply_cif_restraints.restraints_file_name=ligand.cif
what would be the correct syntax to add ligand cif for this
geometry_minimization?
Or what would be the proper way to idealize/optimize a protein structure
with ligands present?
The structure optimization during NMR calculation is not good enough in my
case.
Thanks!
Charles
***************************************************
Charles Chen
Research Instructor
University of Pittsburgh School of Medicine
Department of Anesthesiology
******************************************************
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