VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Wed Oct 31 2018 - 14:52:09 CDT

Thanks Joshua for that help! I also made it work with "serial" and then the atoms' serial numbers. Maybe you could help me with this question:

 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: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
Sent: Wednesday, October 31, 2018 1:20:13 PM
To: McGuire, Kelly; vmd-l_at_ks.uiuc.edu
Subject: RE: Dynamic Bonds Question

Hi Kelly,

Dynamic bonds only account for the distance between the atoms. I'd encourage you to label the two atoms between which you expect to see a bond, so that you can track the distance. The other thing to keep in mind is that dynamic bonds are only drawn between atoms that are within a selection. "type Cu and type NR2" will always contain zero atoms, since an atom (atomselections act on atoms!) cannot have two distinct types simultaneously. Try "type Cu NR2" or the equivalent "type Cu or type NR2". Basically, use a VDW or another obvious representation to make sure you are selecting the correct atoms, and then dynamic bonds will work.

-Josh

On 2018-10-31 12:56:38-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

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