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: [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
