VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Thu Jan 03 2008 - 15:17:54 CST

Or hydrogens for docking studies... Many of the docking programs need
only polar hydrogens, so that might be another option.

In any case, I agree with Peter on using Molefacture. If you will
perform docking, then you should definitively use an extra
software/utility to remove the hydrogens you don't need.

Cheers,
Michel

On Jan 3, 2008 10:25 PM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> 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
>