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

Justin Lemkul jalemkul at vt.edu
Sat Dec 15 20:21:22 CET 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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