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#875 - 01/30/04 01:24 AM Adding counter ions
tjaart Offline
Forum Member

Registered: 10/16/03
Posts: 40
Loc: Pretoria, South Africa

I seem to need to add counter ions to my models to attain an overall charge of 0. How do I do this? Do I simply add in some ions like a Na+ to negate negative charges? Or do I add counter ions in a specific way? Is there a script example in the archive? Can I simply add a ion to the PDB file?

Any help or suggestions welcome!

Tjaart de Beer

#876 - 01/30/04 02:05 AM Re: Adding counter ions [Re: tjaart]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
Hi Tjaart,

Having an electroneutral system is not strictly necessary (execpet perhaps when you use Ewald summation?), but since it is assumed to keep referees from asking why the system is not neutral one often adds enough counter ions to get a zero total charge...

Set up your system as usual, protein+ligand+water, then decide on a number of water molecules to be replaced by ions; you can pick these waters at random, or use some procdure to compute the Coulomb energy of each water oxygen (inte sele type oh2 .and. resi xxxx end sele .not. resi xxxx end) and replace those with the highest energy (if you have to add positive counter ions), or any other method that you may find suitable in your case.

Once you know which waters to replace there is a short script (add-ions.str) that can be used for the actual replacement. See also run-sdb-md.inp for an example of how to use this script.

Best regards from -5C and snowing,

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden


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