Hello Rafael--
> I am trying to determine the structure of a peptide from NOE
> constraints. For this purpose, I used the following scripts which
> did not include the terms corresponding to the dihedral angles of
> the force field, i.e., it did not include the term "DIHE". Thus the
> structures obtained for one of the compounds presented values of Phi
> and Psi that are outside the Ramachandran diagram.
>
> I tried to solve this by including the term "DIHE". When I did that
> many NOE restraints gave problems, and by reviewing them and
> weakening some of them I got structures that do get into the allowed
> zones of the Ramachandran map but are very different from each
> other.
>
> Is there any problem with using the DIHE term? How to solve the
> problem of the dihedral angles or the high RMSD in the structures?
Persumably, your peptide contains natural amino acids. In this case I
suggest uncommenting the TorsionDB setup in your script:
from torsionDBPotTools import create_TorsionDBPot
torsionDBPot = create_TorsionDBPot('tDB')
potList.append( torsionDBPot )
rampedParams.append( MultRamp(.002,2,"torsionDBPot.setScale(VALUE)") )
The reference is given below. This term is the dihedral portion of the default
Xplor-NIH force field, and will aid in keeping backbone phi/psi in
Ramachandran regions, and keeping sidechains rotameric.
Stricter restraints can be introduced using the DihedralPot.
https://bit.niddk.nih.gov/xplor-nih/doc/current/python/ref/dihedralPotTools.html
The DIHE term is appropriate for use in some circumstances, but the
parameters are not configured in the default protein force field. It
is used, for instance, in explicit water refinement.
best regards--
Charles
Reference:
Bermejo, G.A., Clore, G.M., and Schwieters, C.D. (2012). Smooth statistical
torsion angle potential derived from a large conformational database via
adaptive kernel density estimation improves the quality of NMR protein
structures. Protein Sci. 21, 1824-1836.
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