[gmx-users] Small molecule with transition metal (Fe)

[Alessandra Villa]

Hi,


On Mon, Dec 16, 2019 at 10:22 PM Venoos Amiri Roodan <venoosam at buffalo.edu>
wrote:

> Hi,
>
> I am trying to do molecular dynamic analysis for the combination of small
> molecule with Fe, Heme with Fe and eventually do YbtFe(III). I am having
> difficulties assigning the right forcefield for the iron atom.
>
>
Concerning the quality of the force field, the best is to have an overview
of the literature.


> I am wondering if anyone can help with the input file for iron forcefield
> (e.g. itp file). There are limited literature for this kind of simulation
> and I would appreciate if you could help me out with this matter.
>
>
For example GROMOS force field has FE-HEME group defined as [HEME].
To generate itp file, you can try to use pdb2gmx to generate the itp
starting from FeHEME pdb file where
molecule is labelled as HEME and selecting (for example) gromos53a6
Best regards
Alessandra



> Thanks and regards,
> Venoos
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