Hello Junhui-- > > I am doing ensemble refinement with PRE restraints using the fit.py script > file. My protein is hexamer with flexible tails. I found that during the > cooling > steps, the VDW energy was very large and the time step is very small. > Following > is an example. > *--- Dynamics ---- step= 300 ---- time= 0.021599 ---- delta_t=9.3514e-05 > --* > | E(kin)+E(poten)= 31384.160 E(kin)= 576.838 temperature= > 50.113 | > | E(poten)= 30807.3227460 grad= 34.6660233 ANGL= > 5162.0899430 | > | BOND= 1152.4255825 IMPR= 1012.4482395 PRE= > 2831.6677982 | > | RAMA=-21179.4077831 VDW= 41828.0989658 > > The starting structure was refined with no nonbonded violations and small VDW > energies as below. > *-- POWELL ------ step= 135 --- stepsize= 0.01000 --- energy evals= 44 > -* > | E(poten)= -929.6124511 grad= 1.8164828 ANGL= > 1041.7818070 | > | BOND= 226.5438108 IMPR= 137.7415772 RAMA= > -3098.5804725 | > | VDW= 762.9008263 > | > *------------------------------------------------------------------------------* > > Is that possible that the VDW energy so high that the PRE energy can not be > refined? >
I suspect the problem is with copies of the tag interacting with each other. I strongly suggest that you instead work from this script in the Xplor-NIH distribution: eginput/pre/refine/newRefine.py and do write back if you continue to experience difficulties. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
