[gmx-users] Covalent bond/crosslink formation with calcium

[Justin Lemkul]

On 2/2/15 7:08 AM, Turgay Cakmak wrote:
> Dear Gromacs users,
>
>
> We are simulating a large nanofiber assembly composed of repeating units of
> peptides, and we have been trying to see how the addition of calcium would
> affect its behavior. We have already tried adding calcium ions in a random
> distribution, which we successfully did.
>
>
> But we also would like to insert calcium ions directly within the fiber
> structure, near areas with negative charges that the calcium cation can
> potentially bind. Is such a configuration possible (or sensible) to
> simulate in Gromacs?
>

Anything is possible.  You'll have to justify if it's sensible :)

>
> Likewise, we would like to specify a number of covalent bonds between some
> of these side chains and the calcium ions, representing a well-crosslinked
> system. Is this possible, and if so, do you know of a suitable set of
> calcium forcefield parameters for the task?
>

I have never heard of such bonded parameters.  People usually just modify 
nonbonded parameters to get proper coordination geometry.  Divalent metal ions 
are quite tricky, and most force field parameters are pretty bad approximations 
of the true nature of the actual interactions.

You'll almost certainly have to derive suitable parameters, which will involve 
reparametrization of charges, because charge-transfer effects would be 
significant in such a complex.  Simply slapping a covalent bond between some 
peptide group and an ion with +2 charge is likely too crude to be realistic.

-Justin

-- 
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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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