VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 20 2006 - 15:02:37 CST

Lubos,
  A few notes about this. Make sure you don't have any bizarre atom names
that are confusing VMD, as the 'measure hbonds' code depends on correct
identification of the atom names currently. A quick test for this is to
display just the hydrogens with the selection "hydrogen" and make sure you're
getting what you expect.

The order of $selection1 and $selection2 matters. If you provide both,
then $selection2 is treated as the list of acceptor candidates.
When using 'measure hbonds', you should avoid having the same atom listed
in both the $selection1 and $selection2 parameters if you desire to have
reliable results, there's a warning about this in the manual as you've
already noted.

I didn't write this particular routine and haven't had time to analyze it
closely, but just taking the source code and documentation comments at
face value this may explain the results you're getting.

Here's the doc page that describes this briefly if anyone's curious:
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.4/ug/node122.html#6866

  John Stone

On Wed, Jan 18, 2006 at 05:13:29PM +0100, Mgr. Lubos Vrbka wrote:
> hi guys,
>
> i encountered an issue with measure hbonds command:
>
> i use
> set ow [ atomselect top "name OW" ]
>
> measure hbonds 2.9 30.0 [ atomselect top "index 5" ] $ow
> 5 is one of the oxygens contained also in the 'ow' list
> this gives me correct answer (i checked it in the structure)
>
> {5 5} {191 473} {1 0}
>
> however when i reverse the order
> measure hbonds 2.9 30.0 $ow [ atomselect top "index 5" ]
> i get "more than i expected":
>
> {989 5 5 815} {5 191 473 5} {989 1 0 810}
>
> according to the manual it should report index 5 as an acceptor only...
> since there are no other atoms in the 'acceptor' list that could mix
> together with atoms from 'donor' list.
> is this the case where overlapping donor and acceptor cause problems (as
> reported in the manual)? in my case i want to get all hydrogen bonds
> that a given molecule forms, i thought i could concatenate outputs from
> both abovementioned commands, but it doesn't seem to work... or is the
> second command exactly the thing i'm looking for? will it behave the
> same every time?
>
> thanks for help. regards,
> lubos
>
> --
> .....................................................
> Mgr. Lubos Vrbka
>
> Center for Biomolecules and Complex Molecular Systems
> Institute of Organic Chemistry and Biochemistry
> Academy of Sciences of the Czech Republic
> Prague, Czech Republic
>
> http://www.molecular.cz/~vrbka
> ..................................................... 

-- 
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