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

[Najamuddin Memon]

Please obtain topology of calcite (1014) from prodrg and you can also see
protein-ligand simulation protocol of gromacs exactly follow it.

On Tue, Nov 12, 2019, 9:09 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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