[gmx-users] Sigma and Epsilon values for nonbonded interactions with Fe in 2Fe2S cluster

Raj D gromacs.for.f at gmail.com
Wed May 27 17:22:25 CEST 2015

Hi ,
I am currently doing simulation of Fe dependent enzyme using Amber ff and I
too had problem and copied sigma and Epsilon from OPLS ff and so for my
simulation goes on fine.
On May 27, 2015 8:42 PM, "Jan Riehm" <jriehm at bioinformatik.uni-saarland.de>

> Dear users,
> I am using the amber99sb-ildn.ff force field to simulate an adrenodoxin
> molecule in a water box. In it there is a 2Fe2S cluster which is covalently
> bound to four surrounding cysteines (two cysteines to each Fe atom). After
> the first equilibration step (nvt) one of the cysteines clashes or overlaps
> with the farther apart Fe atom (which is not covalently bound). I've
> checked for the nonbonded interaction values in the ffnonbonded.itp and the
> values (sigma and epsilon) for Fe are zero in the [atomtypes]-directive.
> I am pretty new to this MD simulation stuff and want to know how to derive
> the values for epsilon and sigma. Or can I look them up anywhere? Any hint
> to a tutorial would be very helpful!
> Thank you very much and best regards,
> Jan
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