[gmx-users] Adding Na ions to DPPG

Mark Abraham 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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