VMD-L Mailing List
From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Wed Jan 05 2005 - 02:29:52 CST
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On Tue, 4 Jan 2005, Uday Chippada wrote:
UC> Hello everybody,
hello uday,
UC> I am trying to represent (show in graphics window) the hydrogen bonds
UC> formed between two chains using VMD, which means an atom of chain A
UC> has to form a hydrogen bond with an atom of chain B. I dont want to
UC> show the hydrogen bonds formed between atoms of the same chain.
UC> Please tell me how this can be done.
as far as i can tell, this cannot be done with the HBonds
representation directly. i have been asking to have something
similar for DynamicBonds as well for quite some time. but of
course somebody has to program it, and it is a bit tricky to
get it right.
you should be able to do it manually, if you are familiar
with the VMD scripting capabilities.
- you can use 'measure hbonds' to get a list of the hydrogen bonds.
in fact you'll get three lists with the indices of the donor,
acceptor, and hydrogen atoms.
- now you loop through the list and weed out all entries, where
acceptor and donor are from the same chain.
- from the remaining lists you retrieve the coordinates
of the hydrogens and acceptors and then use the graphics
(or draw) command to draw lines between those atoms.
- of course if you want to animate this, you can put it in a subroutine
which can be called via tracing vmd_frame() and then deletes and
redraws everything.
hmmm.... come to think of it, this could be a useful addition to
the collection of vmd scripting on my homepage.
if you can send me (an) example file(s), i may give it a try
since i now have an idea for how to work around my similar
problems with the dynamic bonds as well. ;-)
regards,
axel.
UC>
UC> Sincerely
UC> Uday Chippada.
-- ======================================================================= Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
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