VMD-L Mailing List

From: Brian Radak (brian.radak_at_gmail.com)
Date: Wed Oct 31 2018 - 17:42:53 CDT

Josh is correct - as usual.

I'll just add my favorite QM/MM trick: a CPK representation without bonds
underneath a dynamic bonds representation can be made to look just like a
licorice representation. You can thus get nice movies of bond
formation/breakage (within the distance based approximation).

BKR

On Wed, Oct 31, 2018, 4:14 PM McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> 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*
>
>