VMD-L Mailing List

From: mish (smncbr_at_gmail.com)
Date: Wed Sep 04 2013 - 07:49:44 CDT

Dear all,

I am new to Tcl scripting and thus I need some help regarding pucker value
calculation in VMD. I want to calculate Cremer-Pople (CP) ring puckering
parameters from the AMBER trajectory in VMD. I have all the hexa-pyranoses
in the structures.

I am able to select 6 membered rings by > "ringsize 6 from resid 1". I
found in the mailing lists "$sel get pucker" gives the Hill-Reilly ring
pucker value (should be one non-zero values for 6-membered rings). When I
use "$sel get pucker", it gives 6 values and they all are same(probably one
for each atom). In the article D. Hill & Reilly calculated theta 1, theta
3 and theta 3, three values. But I am surprised that how can a single
Hill-Reilly
pucker value determine three angles characteristic of the conformations ?

If not hen I want to calculate Cremer-Pople parameters for all the rings
and all the frames in trajectory. Cab someone help me if it can be easily
done in VMD somehow ? or if it is described in manual somewhere.

Thanks
Mish