VMD-L Mailing List

From: politr_at_huji.ac.il
Date: Sun Jun 01 2008 - 06:27:48 CDT

Dear VMD users and developers,
Thank you for your generous help.
I have used the angle formed by O-H-----O to be grater than 120 and also
grater than 140 (this definitions are taken from papers). The average
number of hydrogen bonds per water molecule is supposed to be ~3.5. I'm
getting ~4 hbonds when I use 60 and ~3.2 when I use 40.
Do someone has any suggestions
Regina

Peter Freddolino wrote:
> The description of "angle" means that theta - 180 < /angle/, so, for
> example, to get theta > 120 you should use 60 for /angle/. The
> selections you use are just the entire set of atoms that you want to
> search for hydrogen bonds (for example, to get a list of all hydrogen
> bonds matching your criteria in a protein, you would use a selection
> of protein, and then do [measure hbonds 3.0 60 $sel]). There isn't a
> simple way (as far as I know) to access beta; you'd have to
> approximate based on trig identities or write your own script.
> Best,
> Peter
>
> politr_at_huji.ac.il wrote:
>> Dear VMD users and developers,
>> I would like to ask about hydrogen bonds. I saw in VMD manual how to
>> define hbonds: *measure hbonds /cutoff/ /angle/ /selection1/
>> [/selection2/]*: Find all hydrogen bonds in the given selection(s),
>> using simple geometric criteria. Donor and acceptor must be within
>> the /cutoff/ distance, and the angle formed by the donor, hydrogen,
>> and acceptor must be less than /angle/ from 180 degrees.
>> I can't understand the definition of angle. What does it mean "less
>> than /angle/ from 180 degrees". Let say I need the angle formed by
>> O-H-----O (teta in the picture attached) to be greater than 120 what
>> angle should I use in "measure hbonds....." and what selection
>> definitions. What should I do if I need beta (in picture attached) to
>> be less than 30.
>>
>> Thank you in advance
>> Regina
>>
>> ------------------------------------------------------------------------
>>