VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Wed Oct 31 2018 - 13:46:04 CDT

I found that if I use "serial" and the two atoms' serial numbers, then a dynamic bond is drawn with my cutoff selection. This begs the question since I am new to this, what does a dynamic bond really represent if I can arbitrarily select the distance a bond is drawn? I am assuming a Cu-N bond forms at ~2 angstroms, but is there a way to know that the Cu and N are really forming a bond? Is this where looking at the orbitals becomes useful to know that bonding is actually occurring?

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: McGuire, Kelly
Sent: Wednesday, October 31, 2018 11:58:01 AM
To: VMD Mailing LIst
Subject: Dynamic Bonds Question

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