I've cobbled-together an initial model by joining some separate domains. They're all crystal structures on their own, so I think the high energies come from protonating the sidechains, mostly. There aren't any obvious occluded regions. I'm just trying to get minimized initial coordinates. I'm using version 2.39, by the way.
I'm trying to avoid defining a lot of artificial distance restraints and minimizing against them, which I expect would work. "Note that regularize.fixupCovalentGeometry does not enforce VDW interactions unless you set the useVDW argument to True." Yup, I've set useVDW=1. Can you comment on whether I should also set useDynamics=1? By inputting the heavy atoms and protonating them, the energies get very high (with no further dynamics.) The regularize.fixupCovalentGeometry greatly decreases these energies but it seems the VDW term remains high. The main chain doesn't seem to move at all and the side chains only very slightly. Here's an outputted PDB header: REMARK summary Name Energy RMS Violations REMARK summary total 2202.19 31964.0 REMARK summary ANGL 792.98 0.375 0.0 REMARK summary BOND 11.27 0.001 0.0 REMARK summary IMPR 96.82 0.244 0.0 REMARK summary RAMA -17.90 REMARK summary VDW 1319.02 31964.0 Thanks for mentioning torsionDBPot. I'll take a closer look at eginput/gb1_rdc/refine.py to see how it compares with my script. Thanks, Ryan On Thu, Aug 27, 2015 at 10:51 AM, Bermejo, Guillermo (NIH/CIT) [E] < [email protected]> wrote: > 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 >
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