Direct use of weighted Quantum Chemical Energy for ligands in BUSTER refinement:

QM command line options

  • These options are common for both autoBUSTER refine and gelly_refine (geometry regularization).
FlagExplanation
-qm XXX Turn on QM representation for all residues with type XXX and specify that XXX carries no net charge. For instance if your ligand has residue type VIA (iso Viagra) use -qm VIA. If there is more than one VIA present in the structure then a separate QM group will be created for each one.
-qm REA-1 Turn on QM representation for all residues with type REA (retinoic acid) and specify that REA carries a net charge of minus one.
-qm YYY+1 Turn on QM representation for all residues with type YYY and specify that YYY carries a net charge of plus one.
-qm FOO+1,BAR-1 Turn on QM representation for all residues with types FOO and BAR and specify that FOO and BAR carries a net charge of plus one and minus one, respectively.
-qm_weight Z Change the weight for the QM representation in refinement. Z must be a positive number. Default QM weight is 16.0 because this seems to work well.
-qm_helper prog Use a QM helper executable other than the default fdynamo included as part of the BUSTER distribution. The helper program must be specified with a full path name.
-qm_method meth Specify the QM method to be used. The available methods depend on the helper. The default method is 'AUTO'. See links below for more information

Page by Oliver Smart 03 Feb 2011. Any questions regarding our software or this wiki should be directed to buster-develop@globalphasing.com