VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Wed Oct 31 2018 - 12:58:01 CDT

I simulated a copper ion near 4 histidines using QM/MM for 100 picoseconds. I used PM7 in MOPAC. The QM region included the copper ion, some water molecules, and all of the atoms of the four histidine sidechains. The job ended normally. Now, I am trying to analyze the results in VMD. The copper moves close to one of the unprotonated delta nitrogens of the imidazole ring. I tried viewing dynamic bonds for the copper and that nitrogen with a cutoff of 2.1 angtroms, but I do not see a bond. Now, I learned from literature that a Cu-N(imidazole) bond formation is on the ~1 nanosecond timescale. What information does the dynamic bond representation take into account for drawing a bond? Just the distance? Or is this a timescale issue?

I tried for the dynamic bond representation :

type Cu and type NR2

name Cu

name ND1 and segname PP3

type Cu

name ND1 and segname PP3

No dynamic bond shown with these selections. Is there a specific atom selection in the representations that I need to do for atoms of different residues or for metal atoms and non-metal atoms? Thanks!

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602