[gmx-users] Adding Na ions to DPPG

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 27 15:12:18 CET 2008

Peyman Yamin wrote:
> On Monday 27 October 2008 14:08, Mark Abraham wrote:
>> 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.
> Right, but can't I have them all included in a single top??
> What shall I put into the topology of the cation then? I have a single DPPG 
> molecule in water/octanol. So I thought I might just embed the Na inside the 
> DPPG top. in the end DPPG HAS a Na actually, though non-bonded!

Alright, now I understand.  So you will have several different topologies to 
deal with.  You don't need to merge DPPG/Na+ into one!  You have separate 
topologies for water and octanol, too, don't you?  You could use the topology 
from PRODRG as dppg.itp, for example, and construct a .top that has the following:

#include "ffG43a1.itp"
#include "dppg.itp"
#include "spc.itp"
#include "octanol.itp"
#include "ions.itp"

[ molecules ]
NA+	1

All bonded and non-bonded parameters will then be read from the appropriate 
force field files, without merging anything!


> If I'm way away from making sense then would be happy to know the logical way. 
> about genion I thought it's mainly for adding the ions to the solvent, but I 
> should have exactly one Na. 
> Be well,
> Peyman
>> Mark
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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