On Monday 27 October 2008 14:03, Justin A. Lemkul wrote: Actually I'm doing a funny mistake telling I should replace an O with an Na! (probably because of high adrenaline level in my blood for the deadline is near!) I should just put one Na beside the O I have! I simply have a PO4 where one O has no H and thus is negative. an Na+ should accompany this O.
> 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. 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: > > Are you trying to replace the O in DPPG with Na+? Or are you simply trying > to add ions to the surrounding solvent (water)? If you just need ions in > the solvent, use genion; you don't have to do it manually. > > > * 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 ? > > Again, I'm not clear on what you're trying to accomplish. If you replace > one of these oxygen atoms, you will likely not have an integer charge > within the DPPG molecule itself. > > > * 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? > > Simply #include "ffG43a1.itp" at the top of your .top file; it will include > nonbonded and bonded parameters for all the atoms in the system. > > -Justin > > > 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: [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
