Hi Jakob, Please, note that the RAMA term will not help you with inter-chain contacts as it applies to residues within a chain. In particular, the 4D terms that you added are long range in the sense that the angles involved span more than one residue (again, such residues are in the same chain).
When you treat each monomer as a rigid body, the torsion angles won't change, and you will always get the same RAMA energy, as is your case. I hope this helps. Best regards, Guillermo A. Bermejo ________________________________________ From: Jakob Toudahl Nielsen [[email protected]] Sent: Monday, October 18, 2010 11:04 AM To: xplor-nih at nmr.cit.nih.gov Subject: [Xplor-nih] RAMA inter-residue 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) _______________________________________________ Xplor-nih mailing list Xplor-nih at nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
