[gmx-users] How to produce "gro" format for calcite {1014} structure.

[Alessandra Villa]

Hi,
Maybe you could try to convert the cif format to pdb format, if you feel
that your conversion from cif to gro format is not working.
Best regards
Alessandra

On Tue, Nov 12, 2019 at 5:09 PM Hamid Zaree <hamidzaree11 at gmail.com> wrote:

> Hi.
> I would like to simulate Calcite structure in GROMACS. How could I make the
> structure of Calcite {1014}. And how could I make its topology.
> I was found a cif file in AMCSD data bank and a python script which
> produced a favourable shape of Calcite "gro" file; but:
>
> 1- The downloaded "Cif" file is not 1014 symmetry structure.
> 2- The final "gro" file (after implementing that python) has not molecule
> type and unfortunately, all Oxygen atoms as well the "Ca" and "C" came
> along each other and each Oxygen atom considered as a molecule in this
> "gro" file. In this case, I wasn't able to make a proper topology file. by
> any means.
> Special thanks!
> Shahryar.
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