VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_gmail.com)
Date: Tue Oct 05 2010 - 11:33:03 CDT

Charlotte,

in the mode you're using measure hbonds, the selection you feed the
measure hbonds command should contain acceptors AND donors. Try as
selection something like "same residue as (within 5 of residue 5)".
This will make sure, you take all the residues within 5 A of your
residue 5 into the selection. measure hbonds will then find hydrogen
bonds within this selection.

eddi

On Tue, Oct 5, 2010 at 10:35 AM, <charbott_at_gmail.com> wrote:
> 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
>>
>>
>> 

-- 
--
=============================================================================
Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078
http://www.ks.uiuc.edu/~eschrein/
=============================================================================