[gmx-users] Adding Na ions to DPPG

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 27 14:03:51 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. 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:

Are you trying to replace the O in DPPG with Na+?  Or are you simply trying to 
add ions to the surrounding solvent (water)?  If you just need ions in the 
solvent, use genion; you don't have to do it manually.

> * 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 ?

Again, I'm not clear on what you're trying to accomplish.  If you replace one of 
these oxygen atoms, you will likely not have an integer charge within the DPPG 
molecule itself.

> * 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? 

Simply #include "ffG43a1.itp" at the top of your .top file; it will include 
nonbonded and bonded parameters for all the atoms in the system.


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


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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