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!
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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