[gmx-users] Constraint of active site in gromacs

[Raj D]

Thanks Justin , but I have a modelled protein download from Modbase and
added Fe iron into the approximate ligating distance of three ligating
atoms of the amino acids. Now I am aiming to bring the octahedral geometry
of the Fe coordinating atoms which include two more water molecules using
EM engine of Gromacs. Will it be possible to let the EM to optimize the
distances between the atoms of the octahedral by constraining the angles
and positions of the atom positions for a octahedral geometry ?
Regards,
Raja
On May 6, 2015 5:14 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 5/6/15 3:09 AM, Raj D wrote:
>
>> Dear User,
>> I would like to constraint the Iron bound active site of the protein in
>> octahedral shape in EM and MD steps ... Is there a direct routine to
>> create
>> such a constraint in gromacs by feeding information of ligating atoms of
>> amino acids with Iron at the center of the octahedral geometry.
>>
>
> What you need are distance restraints, which you will have to write in the
> topology yourself.
>
> -Justin
>
> --
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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