Dear Juzer
This is a VMD question, NOT an amber question. Please send it to the VMD
mailing list.
Adrian
On 5/1/11 5:15 PM, juzer stationwala wrote:
> 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.
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project, Department of Chemistry
University of Florida
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
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Received on Sun May 01 2011 - 08:30:04 PDT
