[gmx-users] Adding Na ions to DPPG
Peyman.Yamin at cbi.uni-erlangen.de
Mon Oct 27 15:19:46 CET 2008
On Monday 27 October 2008 15:12, Justin A. Lemkul wrote:
> 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 ]
> DPPG x
> SOL y
> OCT z
> NA+ 1
> All bonded and non-bonded parameters will then be read from the appropriate
> force field files, without merging anything!
Hey this looks beautiful! I'll try it right away!
> > 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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