[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

[Justin Lemkul]

On 12/15/12 2:18 PM, James Starlight wrote:
> So as I understood  it've happened because the conformation of the
> adjacent residue is differ when that residue bounded to the
> chromophore ( in comparison to the residue in unbound capped form).

Conformation is irrelevant; atom types are all that matter here.

> But in term of the backbone geometry of C and N-terms chromophore is
> like a typical amino acid. Also Chromophore is defined as a protein in
> the residue.dat.  When I've examined error log of my system I've
> noticed that missing UB and dihedral parametrs of the i+1 residue have
> never present in the ffbounded.itp ( the exact combination of the
> triplet and quadruplet of atoms for UB and dihedral). Is there any
> other ways to define termi of my non standard residue as the standard
> one?
>

If a particular bonded interaction is not present in the parent force field, you 
have to derive it parameters for it.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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