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! 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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
