[gmx-users] Energy minimising structures containing metal ions

[david lawson (JIC)]

Dear All,

I am a GROMACS novice looking for some advice. 

I have a crystal structure with a ligand bound and an unoccupied metal
site. I have manually inserted Mg2+ in the latter and would now like to
energy minimise the whole structure mainly to improve the geometry at
the metal site (a few side chains need to move). Ultimately I want to
dock a second ligand into the structure that should interact with both
the first ligand and the Mg2+ (for this I will use Autodock4). 

I have come across a few useful tutorials on the web, but not so far
seen anything that deals with energy minimising complexes involving
metal ions. I would be most grateful if anyone could provide me with
some example files (especially .mdp files) or point me in the direction
of any other relevant material on the web.

Many thanks in advance,

Dave Lawson 

-------------------------------

Dr. David M. Lawson
Biological Chemistry Dept.,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Fax: +44-(0)1603-450018
Email: david.lawson at bbsrc.ac.uk
Web: http://www.jic.bbsrc.ac.uk/staff/david-lawson/index.htm