From: Axel Kohlmeyer (
Date: Fri May 28 2010 - 08:30:34 CDT

On Thu, 2010-05-27 at 16:21 +0100, Jennifer Williams wrote:
> Hi,

hi jenny,

> I have a cif file of a metal organic framework. There is water
> coordinated but the XRD generated cif files only has the positions of
> the oxygens, not the hydrogens.
> Can someone recommend a *free* software which can do a hydrogen adjust
> and then a minimisation/optimisation to find the positions of these
> hydrogens whilst keeping all the known atoms fixed? Can VMD do this? I
> know Materials Studio can do this but I don't have access to this.

VMD is as such not a modeling tool and it definitely has no
knowledge of chemistry to be able to tell which hydrogen would
be missing where (sometimes even chemists have trouble with that).
there are add-on tools like psfgen that work via a residue
database or molefacture that work interactively.
none of those can do a minimization, you'd have to use NAMD
or some other MD code for that. there are quite a few open source
molecular editors that have some features along those lines, but
so far none of them has been very convincing. the avogadro project
seems to be very promising, but the last time i tried it was
segfaulting on me all the time as soon as i tried something more
complex than just loading a simple file or building a simple molecule.

hope that helps,

> Thanks
> Jenny

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.