In message <[EMAIL PROTECTED]> (on 12 September 2008 15:25:38 +0200), [EMAIL PROTECTED] (Jochen Hub) wrote: >sarbani chattopadhyay wrote: >> >> Hi everybody, >> I want to add counter ions based on potential and not randomly. >> I will be very grateful if anyone can guide me through the command >>"genion" for this. > >As far as I know, that has not been implemented yet. It is a good idea, >though.
I've written a perl program to do this for a limited case (addition of +1 ions only, just with respect to proteins and NADPH (NDP), based on whole charges); see http://cesario.rutgers.edu/easmith/research/ (under the perl programs) for check.water.for.pos.ions.pl. This program actually takes a PDB file with waters added - see add.water.for.ions.pl for one program with an example in it for how to do this; the "editconf" mention in it is because it's preferable to do this with a centered protein. It then tells you the best places to replace oxygens from water with positive ions; you can then translate the PDB file back into gromacs format (ideally after adding hydrogens again with something like the Richardsons' "reduce" program). -Allen -- Allen Smith, Ph.D. http://cesario.rutgers.edu/easmith/ February 1, 2003 Space Shuttle Columbia Ad Astra Per Aspera To The Stars Through Asperity _______________________________________________ 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
