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

[Justin Lemkul]

On 11/14/19 4:03 AM, Najamuddin Memon wrote:
> Please obtain topology of calcite (1014) from prodrg and you can also see
> protein-ligand simulation protocol of gromacs exactly follow it.

PRODRG produces topologies of very poor quality and does not support 
calcium.

-Justin

> 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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