From: Axel Kohlmeyer (
Date: Mon Aug 25 2008 - 14:56:41 CDT

On Mon, 25 Aug 2008, nahren manuel wrote:

NM> Dear VMD users,

dear nahren,

NM> I am new and this is my first email to this group.

NM> I calculated the hbonds between my amino acid ( asp 88) and solvent
NM> molecules surronding the same. When i analysed my trajectories ( in
NM> a random manner), I noticed that this water molecule , the one
NM> hydrogen bonded to asp 88 , was also h-bonded to another main chain
NM> CO ( of val 90). I did not know how to select this water molecule
NM> and check if this is hbonded to CO ( of Val 90) .

you have to give some more detail of what you want to achieve.
are you talking about a visualization or just text mode/scripting
info? the vmd selection language allows you very flexible selections
of atoms, you just have to combine them with "and" and "or" and
you can probably construct something based on that.
alternately, you can check the list of h-bond donors and h-bond
acceptors for multiple entries of the same atom index.


NM> warm regards,
NM> nahren

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.