[gmx-users] to add counter ions based on potential

Allen Smith easmith at beatrice.rutgers.edu
Fri Sep 12 20:30:57 CEST 2008

In message <48CA6DD2.5050500 at gwdg.de> (on 12 September 2008 15:25:38 +0200),
jhub at gwdg.de (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,

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 Smith, Ph.D.                http://cesario.rutgers.edu/easmith/
February 1, 2003                               Space Shuttle Columbia
Ad Astra Per Aspera                     To The Stars Through Asperity

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