VMD-L Mailing List

From: charbott_at_gmail.com
Date: Tue Oct 05 2010 - 10:35:14 CDT

So I think what I'm confused about is making a selection with the acceptors
and donors. I was using index because that way I knew for sure I was not
selecting hydrogen atoms, and I had seen in previous examples people doing
the same thing.

I'm trying to find the residues a specific residue is hydrogen bonded to. I
know that the output will tell me this, but I keep getting empty arrays. It
doesn't matter what selection I use, such as "chain A and resid 5." Could
someone give me an example of a selection that would work? I think that
will help clear things up for me.

thanks
Charlotte SIska

On Oct 4, 2010 4:09pm, Pat Yee <pyee_at_nd.edu> wrote:
> 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