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
--
========================================
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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