Amanda, X2TOP is a somewhat enigmatic tool. You are never sure when it why it works or refuses to generate a topology...
Try to start with PDB file instead of GRO. Try to use -"pbc" keyword. Try to add new lines to N2T database corresponding to all atoms of your molecule. Good luck, Vitaly > I have tried to convert this file to a top file but this is the error message > I > get: > > Opening library file /usr/share/gromacs/top/aminoacids.dat > WARNING: masses will be determined based on residue and atom names, > this can deviate from the real mass of the atom type > Opening library file /usr/share/gromacs/top/atommass.dat > Entries in atommass.dat: 178 > WARNING: vdwradii will be determined based on residue and atom names, > this can deviate from the real mass of the atom type > Opening library file /usr/share/gromacs/top/vdwradii.dat > Entries in vdwradii.dat: 28 > Opening library file /usr/share/gromacs/top/dgsolv.dat > Entries in dgsolv.dat: 7 > Opening library file /usr/share/gromacs/top/electroneg.dat > Entries in electroneg.dat: 71 > Opening library file /usr/share/gromacs/top/elements.dat > Entries in elements.dat: 218 > Looking whether force field files exist > Opening library file /usr/share/gromacs/top/ffoplsaa.rtp > Opening library file /usr/share/gromacs/top/ffoplsaa.n2t > Opening library file /usr/share/gromacs/top/ffoplsaa.n2t > There are 23 name to type translations > Generating bonds from distances... > atom 48 > Can not find forcefield for atom C-4 with 2 bonds > > ------------------------------------------------------- > Program x2top, VERSION 4.0.7 > Source code file: ../../../../src/kernel/x2top.c, line: 207 > > Fatal error: > Could only find a forcefield type for 47 out of 48 atoms > ------------------------------------------------------- > > "Throwing the Baby Away With the SPC" (S. Hayward) > > I have tried to adjust the coordinates within the gro file but it still shows > the same message. Someone please give me some proper instruction in the > conversion of a .gro file to a .top file. Thank you! > > Sincerely, > > Amanda M. Watkins > > SBC 2012 -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php