VMD-L Mailing List

From: Uday Chippada (chippada_at_eden.rutgers.edu)
Date: Thu Sep 23 2004 - 13:53:51 CDT

Hey all,

I have a wierd problem with Graphical representation of hydrogen bonds. When I select drawing method as HBonds, and give a Distance cut off of 2.6, only hydrogen bonds with a length of less than 1.7 A are shown in the Display window. If I increase the cut off to 3 then only hydrogen bonds with length less than 2.3 -2.4 A are shown on the display window. I have used the TCL script (hbond.tcl) that Ahmet has so generously provided on the list a few days ago, to calculate the number of hydrogen bonds, and found that the script returns a lot more hydrogen bonds than what is being shown on the display screen.

It would be great if anyone has any comments or can tell me what exactly is being represented on the display window.

Thanx in advance
Uday.