[gmx-users] mismatch sol.gro/topol.gro

[Francesco Pietra]

I understand that transferring a system organized for namd-charmm36 ro
gromacs-charmm36 involves blind usage of transformation tools that are not
from gromacs. In the specific case, the tool became confused by the ligand
having a side chain with hyphened atom numbering, should the mismatch
between atom number depends from that. It proved also difficult using
qm-improved stream files from CGenFF for such transformation tools.
So that, I decided not to try further with gromacs-charmm36, going back to
namd-charmm36, also not to overload the mailing list with too many
requests. I thank you very much users and maintainers for the much aid I
received. In spite of unsuccessful work, i am happy to have had the
opportunity to see how the preparation for gromacs is carried out.
cheers
francesco pietra

On Wed, Nov 28, 2018 at 6:42 PM Francesco Pietra <chiendarret at gmail.com>
wrote:

> I am preparing (as a newcomer to gromacs) a complex of a protein with two
> ligands. One is the universal GDP, the other one a diterpenoid. GROMCS2018,
> CGenFF, CHARMM36.
>
> The output of addions complains about GDP.prm (the GDP.str of CGenFF
> origin had no problems for NAMD/CHARMM36) and (because of this, or not)
> there is a mismatch of ion number
> Fatal error:
> number of coordinates in coordinate file (complex_solv.gro, 51025)
>              does not match topology (topol.top, 51137).
>
> Attached the full output. Grateful for advice
>