From: juzer stationwala (
Date: Sun May 01 2011 - 10:31:55 CDT

Hello VMD users,
I have carried out H-bond analysis of my AMBER-10 trajectory file using
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

thanks a lot to all.

Warm Regards:
Juzer Stationwala,
Dept. of Pharmacoinformatics,
National Institute of Pharmaceutical Education & Research