[gmx-users] Re: using x2top to convert a gro file to a top file

[Vitaly Chaban]

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