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

[Justin Lemkul]

On 6/14/16 7:37 AM, Marlon Sidore wrote:
> 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.
>

You should contact the corresponding author of the paper.  This is not a GROMACS 
problem.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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