[gmx-users] Adding Na ions to DPPG
Mark.Abraham at anu.edu.au
Mon Oct 27 14:08:30 CET 2008
Peyman Yamin wrote:
> Dear GMX users,
> I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure
> with the Na replaced with O.
That doesn't make sense to me.
> I get a .top with this from prodrg and try to
> add the Na manually at the right place by removing the corresponding O. I use
> GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem:
> * In .top file, as far as I can understand, I should just replace OA with NA+
> and set the mass and charge.
> DPPG has a centre: [ O-P(O)=O ] -
> The Na+ should be around this with +1 charge.
> should I put charge +1 ?
> * which parameters should I place in the top as the Na+ is not bonding. I need
> LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA)
> but I'm not sure where should I put it in the top file. What should I insert
> manually in top file at all?
Sodium is not going to form any bond. It's a labile ion, so needs its
own [ molecule ] section. The easiest approach is to construct a
topology for the anion, and then use genion to add suitable amounts of
Na+ afterwards. Check out some tutorial material for the approach here.
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