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
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