[gmx-users] Adding Na ions to DPPG

Peyman Yamin Peyman.Yamin at cbi.uni-erlangen.de
Mon Oct 27 15:02:06 CET 2008

On Monday 27 October 2008 14:03, Justin A. Lemkul wrote:

Actually I'm doing a funny mistake telling I should replace an O with an Na! 
(probably because of high adrenaline level in my blood for the deadline is 
near!) I should just put one Na beside the O I have! I simply have a PO4 
where one O has no H and thus is negative. an Na+ should accompany this O.

> 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.
> -Justin
> > 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

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