VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Jan 03 2008 - 14:25:05 CST

Certainly, although the best way to do this depends on exactly what
you're adding the hydrogens for. If you want to do an MD simulation, or
want to add hydrogens to a complete biomolecule for which a charmm
topology is present, generating a psf will add hydrogens (you can see an
example of how to do this in the namd tutorial). If you just want to add
a few hydrogens to a ligand for some other purpose, you can use the
molefacture plugin (Extensions->Modeling->Molefacture) to edit bond
orders and add hydrogens (I'd recommend making sure you have an up to
date version of vmd if you use this).

Best,
Peter

snoze pa wrote:
> Dear Vmd users,
> Is it possible in vmd to add hydrogen atom to protein or ligand? any help
> thanks in advance and happy new year
> s