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: [EMAIL PROTECTED] Web: http://www.jic.bbsrc.ac.uk/staff/david-lawson/index.htm _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
