Justin, As i understood from reading and tutorial what i should do is, lets say i generated a topology file named as topol.top, so i need to add #include "oplsaa.ff/ions.itp" so it accounts for Na+.
my question is.. 1.how can i get rid of sodium? just removing the corresponding lines from the .pdb text? 2. i tried with uncharged system for simplicity with less number of atoms..( here i replaced the COONa functional group with a CH3 group) but still g_x2top -f test.pdb -o np1.top -name np1 -ff oplsaa -pbc am getting this parameters missing.. Can not find forcefield for atom C-147 with 1 bonds Can not find forcefield for atom C-148 with 1 bonds Can not find forcefield for atom C-873 with 1 bonds Can not find forcefield for atom C-874 with 1 bonds Can not find forcefield for atom C-939 with 1 bonds Can not find forcefield for atom C-940 with 1 bonds Can not find forcefield for atom C-1137 with 1 bonds Can not find forcefield for atom C-1138 with 1 bonds Can not find forcefield for atom C-1269 with 1 bonds Can not find forcefield for atom C-1270 with 1 bonds for that do i need to modify the atomname2type.n2t the way i did earlier?or am i doing this wrong? -- View this message in context: http://gromacs.5086.x6.nabble.com/OPLS-force-field-issue-tp5013353p5013406.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
