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! > > -Justin >
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 > >> _______________________________________________ > >> gmx-users mailing list [email protected] > >> 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 [email protected] 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
