[gmx-users] Non-neutral system with iron-sulfur clusters

[Marlon Sidore]

I checked everything and even by adding the numbers on the paper and the
cystein charges from amber03 (the FF they used in the paper) the resulting
charge isn't an integer.

The paper has charges for the Fe (4x), the S (4x) from the cluster, the S
from the CYS bound to it and the CB bound to the previous S in CYS. Simply
adding them and the other atoms from CYS (4x in case of the CYS atoms)
doesn't yield an integer. I didn't count S and CB twice either.

The resulting charge from the whole 4CYS-4Fe-4S is -1.233684.

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France


2016-06-14 13:20 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 6/14/16 4:59 AM, Marlon Sidore wrote:
>
>> Hello everyone,
>>
>> On my quest to use the parameters for iron-sulfur clusters from [1] I
>> realized that the resulting clusters are not neutral. Indeed, even though
>> the charges of the 2 CYS atom (SG and CB) are modified, the overall charge
>> of the cluster + the 4 CYS isn't a round number.
>>
>> Should I worry ?
>>
>>
> Non-integer charges are totally non-physical, so using such a topology
> would be wrong.  Check carefully that you've assigned everything correctly.
>
> -Justin
>
> 1. Smith, D. M. A., Xiong, Y., Straatsma, T. P., Rosso, K. M. & Squier, T.
>> C. Force-Field Development and Molecular Dynamics of [NiFe] Hydrogenase.
>> J.
>> Chem. Theory Comput. 8, 2103–2114 (2012).
>>
>> Marlon Sidore
>>
>>
>> PhD Student
>> Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
>> CNRS - UMR7255
>> 31, Chemin Joseph Aiguier
>> 13402 cedex 20 Marseille
>> France
>>
>>
> --
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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>
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