VMD-L Mailing List

From: Pat Yee (pyee_at_nd.edu)
Date: Mon Oct 04 2010 - 17:09:42 CDT

Carlotte,

Try this:

set sel1 [atomselect top "ACCEPTORS"]
set sel2 [atomselect top "DONORS"]
measure hbonds 3.5 30 $sel2 $sel1

Put in appropriate atom selections for your donors and acceptors. Defining
both sets of donors and acceptors as variables might help you with your
problem.

Pat Yee

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Charlotte Siska
Sent: Monday, October 04, 2010 4:02 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: trouble with measure hbonds

Whenever I try to use measure hbonds I get nothing but three empty
lists. I have made sure that the index I use for my selection does not
have hydrogen atoms, which was recommended in other postings in the
mailing list. I think I am missing something.

General code:

measure hbonds 3.5 30 [atomselect top "index 5"]

Any help would be greatly appreciated!

Charlotte Siska