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

[Turgay Cakmak]

Thank you for the swift reply!

We have decided against defining covalent bonds and went with the
calcium-within-peptide-fiber configuration, but we have run into another
problem, in that some of the calcium cations vanish from the unit cell that
the fiber is in, and appear in the next unit cell, when we run an energy
minimization. The missing cations are all on the same side of the peptide
fiber and form a neat half-cylinder on the adjecent unit cell, so we are
fairly certain that the problem has to do with our box definition.

However, the entire structure is within our dodecahedral box prior to
energy optimization. Is there any reason that the calciums would change
position after energy minimization? Do we have to redefine our box
afterwards?

Thanks in advance,
-Turgay

2015-02-02 15:01 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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
>
> --
> ==================================================
>
> 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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