[gmx-users] Adding Na ions to DPPG

[Peyman Yamin]

Dear GMX users,

I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure 
with the Na replaced with O. 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? 

Thanks in advance for the time,
I've been away for some time from GMX and might sound 

Cheers,
Peyman 


-- 
Peyman Yamin
Lehrstuhl fuer Thermische Verfahrenstechnik
Universitaet Erlangen-Nuernberg
Egerlandstr. 3
91058 Erlangen
Phone: +49(0) - 9131 - 85 27671
Mailto: peyman.yamin at cbi.uni-erlangen.de