Hello amber users,
I have carried out H-bond analysis of my 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
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Received on Sun May 01 2011 - 08:30:03 PDT
