Yes, yes... I mixed them up again... One should try that option which is not default.
> Vitaly Chaban wrote: >> >> 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. >> > > The -pbc option is broken in the 4.0.x series and will cause the program to > hang in every case I've seen it invoked. You must use -nopbc to get the > program to complete. > > -Justin > >> 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 > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
