From: Axel Kohlmeyer (
Date: Sat Jan 31 2009 - 17:35:53 CST

On Sun, 1 Feb 2009, Thomas Evangelidis wrote:

TE> Dear VMD users,
TE> is there a scriptable way to add hydrogens? I've read in previous threads
TE> about molfacture and autpsf but I'm not sure if these plugins are
TE> scriptable.


check out the documentation on the web. autopsf is to some
degree scriptable, but in essence it is a scripted frontend
to psfgen so you may be better off harvesting some components
and drive psfgen yourself.

TE> Moreover I would like to display Hbonds between a ligand and the receptor
TE> but not between ligand atoms or receptor atoms. Can I do that with VMD
TE> commands?

it is a bit tricky, since the HBonds rep currently has no
separate selections for donors and acceptors. i've been looking
for having something similar for Dynamics Bonds for more than
five years now.

with some scripting, however, you can work around it by building
a representation for each potential hbond (donor, acceptor,
hydrogen) that you want to consider. not elegant and not fast,
but it works, ...and until now this was always the lesser evil
compared to implementing it myself thanks to large multi-processor
desktops. ;)


p.s.: saw your plugin being integrated into the VMD cvs the other day.
if john hasn't done so already, i can give you some comments on what
you should into to improve it. ;-)

TE> thanks in advance,
TE> Tom

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.