Hi Ryan, Could you describe a bit what you are trying to do?
Note that regularize.fixupCovalentGeometry does not enforce VDW interactions unless you set the useVDW argument to True. Also note that the replacement of RAMA, torsionDBPot, yields slightly fewer clashes. For an example of its setup see eginput/gb1_rdc/refine.py within your Xplor-NIH directory. Best, Guillermo ________________________________________ From: Ryan Hoffman [[email protected]] Sent: Thursday, August 27, 2015 12:49 PM To: [email protected] Subject: [Xplor-nih] high VDW question (and mailing list is offline?) Hi there! https://dcb.cit.nih.gov/pipermail/xplor-nih/ is apparently offline? My question's fairly simple...what is the current state of the art for relaxing VDW violations? The rest of the bonded parameters are good, but there are apparently many, many VDW violations. I have no experimental restraints at this point although I am using the RAMA potential. I've been trying regularize.fixupCovalentGeometry, as well as deleting the hydrogens and rebuilding them, and using Powell minimization following brief (and low-T) dynamics. Especially the former removes all of the violations but they seem to accumulate in the VDW term. Thanks, Ryan _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
