VMD-L Mailing List

From: Rachel (comeonsos_at_googlemail.com)
Date: Tue Jul 31 2007 - 08:42:57 CDT

Dear VMD community,

By using measure contacts cutoff selection1 selection2, all atoms in *
selection1* that are within *cutoff* of any atom in *selection2* and not
bonded to it are listed out. What I want to ask is, does this cutoff
distance include the vdw radius of atoms in selection2? what I want to do is
find the atom list of atoms in selection1 that are with contact(collides)
with atoms in selection2, and I assume they are in contact with each other
if the distance between them are less than the sum of their vdw radii. So if
in selection2 are all carbon atoms (with vdw raidus=1.7Angstrom) and in
selection1 are all oxygen atoms (vdw=1.52 Angstrom), then in my case should
I define the cutoff as 1.52 or as 3.2? thank you for your help.

Kind regards,
Rachel