VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sun May 01 2011 - 11:29:18 CDT

As noted in the manual, "measure hbonds" (and thus anything that derives
from it, like the H bonds plugin), can't be trusted when the two selections
overlap. In your first case, the second selection also includes the ligand.

 

 

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
juzer stationwala
Sent: Sunday, May 01, 2011 10:32 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: question regarding H-bond calculation

 

 

 

Hello VMD users,
I have carried out H-bond analysis of my AMBER-10 trajectory file using
VMD-1.8.7.
I tried two different ways:

Case 1
 I gave the atom selection 1- resname lig
atom selection 2- all not water
Case 2
atom selection 1- resname lig
atom selection2 - protein

In both cases VMD recognises same interactions but the occupancy of a
particular H-bond differs in both cases.

If my suppositions are correct both values of selection 2 implies to same
set of atoms as there are no other molecules involved in my system except
protein, ligand & explicit water molecules.

Can any one give me suggestions why there are different sets of values on
same atoms into considerations & results from which case should be more
acceptable.

thanks a lot to all. 

-- 
Warm Regards:
Juzer Stationwala,
Dept. of Pharmacoinformatics,
National Institute of Pharmaceutical Education & Research 
(NIPER)
Mohali,
Punjab. 
India