Dear Xplor-nih users,
I would like to use the RAMA term for inter-chain contacts, I am
trying to use the following modification to the initialization in
protocol.py:
def initRamaDatabase(type='protein',simulation=0,useinter=False):
...
xSim.command("""eval ($krama=1.);eval ($kramalr=1.)...""")
if useinter:
@QUARTS:2D_quarts_new.tbl
@QUARTS:3D_quarts_new.tbl
@QUARTS:forces_torsion_prot_quarts_intra.tbl
@QUARTS:forces_torsion_prot_quarts_inter.tbl #this is new
@QUARTS:4D_quarts_inter_new.tbl #this is new
end
@QUARTS:setup_quarts_torsions_intra_2D3D.tbl
@QUARTS:setup_quarts_torsions_inter.tbl #this is new
However is seems that inter-residue forces are not active. I calculate
a structure for a symmetric oligomer and all monomer are fixed through
the group statement using rigid body dynamics. However different
supramolecular structure yields exactly the same RAMA energi.
Can someone help me on how to use RAMA for long-range interactions?
best regards,
Jakob
--
Jakob Toudahl Nielsen, post doc
Laboratory for Biomolecular NMR Spectroscopy
inSPIN, Center for Insoluble Protein Structures
Department of Chemistry, University of Aarhus
Langelandsgade 140, DK-8000 Aarhus C, Denmark
Phone: +458942 5528 or +452993 8502 (cell)
