VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Jan 31 2009 - 16:44:37 CST

Hi Tom,

autopsf is quite scriptable; try typing
package require autopsf
autopsf

in the console for usage instructions.

For displaying only ligand/receptor hbonds, you might make to separate
reps, one containing only hbond donors on the protein and acceptors on
the ligand, and the other containing only acceptors on the protein and
donors on the ligand.

Best,
Peter

Thomas Evangelidis wrote:
> Dear VMD users,
>
> is there a scriptable way to add hydrogens? I've read in previous
> threads about molfacture and autpsf but I'm not sure if these plugins
> are scriptable.
> Moreover I would like to display Hbonds between a ligand and the
> receptor but not between ligand atoms or receptor atoms. Can I do that
> with VMD commands?
>
> thanks in advance,
> Tom