[gmx-users] Fe2+ non bonded parameters for AMBER

[Nataraj Balakrishnan]

Dear Justin,
Thanks for your reply. I just came across one article which uses Fe2+ ion
in the active site and as you mentioned they have used phorpherin structure
to mimic the Fe2+ parameterzation but nothing mentioned explecitily other
parameters details. They have used Amber molecular suit for their
simulation. So I don't know how to verify their parameters with my setup
now I am using zn2+ parameters for Fe2+.
Regards,
Raja
 On Apr 15, 2015 5:50 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 4/15/15 12:19 AM, Raj D wrote:
>
>> Dear Users,
>> Had anybody used Fe2+ ions in the active site of protein. I am planning to
>> use one using amber99sb forcefield...please suggest to use the nonbonded
>> parameters for Fe2+ ions, sigma and epsilon values.
>>
>
> Most force field parameters are specifically for heme, so if they haven't
> been developed yet, you're probably out of luck without doing the
> parametrization yourself.  Additive models for transition metals are very
> crude, anyway.  You face the additional challenge of getting the
> electrostatics right.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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