[gmx-users] Adding Na ions to DPPG

Kukol, Andreas a.kukol at herts.ac.uk
Mon Oct 27 14:03:51 CET 2008

Use the Gromacs program genion for that purpose. This replaces water molecules by the ions you specify. You may need to change the topology afterwards manually. Make sure, you put an #include ions.ipt near the top of the .top-file, this contains the force field parameters for ions.

Best wishes

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Peyman Yamin
> Sent: 27 October 2008 12:36
> To: gmx-users
> Subject: [gmx-users] Adding Na ions to DPPG
> 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:
> * 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?
> 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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