[gmx-users] iron sulphur cluster

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 6 14:46:48 CEST 2011

francesco oteri wrote:
> The author of such work  published partial charges, but nothing about 
> other parameters.

In order to carry out any simulation, you need more than charges.  If they did 
any subsequent validation of the charges, they must have assigned these 
parameters.  If they calculated charges and did no validation, then you should 
question whether or not the charges are valid.

> The force-fields used are gromos43A1 and CHARMM22. The GROMACS standard 
> distribution contains nothing about iron sulphur cluster.

Nonstandard additions to force fields are not included in Gromacs distributions.


> Thank you
> 2011/10/6 Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>
>     On 6/10/2011 11:24 PM, francesco oteri wrote:
>         Dear gromacs users,
>         I've to simulate a protein with an 4Fe-4S and a 3Fe-4S iron
>         sulphur cluster.
>         Lot of approaches are present in literature. There are a lot of
>         papaers suggesting partial charges
>         but very few suggestions regarding bonded and not bonded parameters.
>     All such work should describe a source for such parameters, if they
>     are not in the standard force field.
>         So i am wondering if any member of this mailing list can send me
>         a link, a file or something advice can be useful to
>         obtain the topology of a protein with the iron sulphur clusters.
>         It is worth noting that I am not interested in electronic
>         properties so also advice using restraint are ok for me.
>     The authors of such work would be a good place to ask.
>     Mark
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> Cordiali saluti, Dr.Oteri Francesco


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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