VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun May 01 2011 - 11:32:09 CDT

On Sun, May 1, 2011 at 11:31 AM, juzer stationwala
<juzer.niper_at_gmail.com> wrote:
>
>
> 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.

no, you are not correct. in case 1 selection 2 would include the ligand
in case 2 it doesn't.

you can easily verify this on the command line.

cheers,
    axel.

>
> 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
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.