DINOSAUR

• Procedures creating the necessary files:
  • DINOIN : creates or modifies the DINOSAUR input file
  • MKHTYP : creates a proton codes file for the GROMOS programs (DINOEM and DINOMD).
  • MKHCO : creates a proton only file (.mdh) or a proton trajectory file (.hco) from GROMOS coordinates or trajectory files
  • CVNOE : conversion program for NOE trajectories: binary <--> formatted
  • CVHCO : conversion program for proton trajectories: binary <--> formatted

• Special for ensemble refinement:
  • GENENS : generates a GROMOS file containing several solutes (ensemble) by duplicating and shifting one solute or by combining several different solutes.
  • SPLITCO : inverse of GENENS, splits ensemble coordinates files into several files with each one solute molecule.
  • AVNOE : averages NOE trajectories for analysis with ANANOE

• Simulation/refinement procedures:
  • DINODD : NOEs driven dynamics. This program is based on program SHAKE (distances driven dynamic) of Ruud Scheek University of GRONINGEN and works with DG format files.
  • DINOEM : NOEs restrained energy minization based on the GROMOS program PROEML
  • DINOMD : NOEs restrained molecular dynamic based on the GROMOS program PROMDL

• Analysis procedures:
  • RFACAV : Calculation of a set of R-factors from a proton trajectory file.
  • RFACDG : Calculation of a set of R-factors for DG structures.
  • RFACGR : Calculation of a set of R-factors for GROMOS structures.
  • RFACDIS : Calculation of a set of R-factors for DISCOVER structures.
  • RFACPDB : Calculation of a set of R-factors for PDB structures.
  • RNOISE : Calculation of R-factors as function of the experimental errors defined as (NOISE + %err * Aexp)
  • SELPKS : Selection of NOE peaks from input file for analysis with ANANOE (only for 2D DINOSAUR)
  • SELDIM : In case of symetrical dimer, SELDIM selects NOEs from the DINOSAUR input file, duplicates and writes them to a NOE file which can be read in DINOIN. By comparing the theoretical NOE intensities for both possible assignments with the experimental ones a choice can be made if the NOE is intra- or inter- monomer.
  • CHAMB : In case of a symetrical dimer CHAMB check the assignments by comparing the distances and NOEs for both possible assignments (inter or intra monomer). It uses therefore a distance file genrated by the Rfactor calculation and a NOE energy file generated by ANANOE.
  • ANANOE : Analysis of a NOE trajectory in terms of R-factors, residue R-factors, NOE energies ... for a set of selected peaks.
  • CHKASS : Analysis of the results of the dynamic assignment procedure implemented in DINOSAUR

• Special 3D NOE-NOE refinement :
  • GEN3DDIS: Generates qualitative distance constraints from 3D NOE-NOE data

- source dinosaur (instal DINOSAUR procedures)

(source ~albo/dino/csh/dinosaur)

- dinoset (define molecule name)
- dinodir (define or modify working directory)
- dinoin (create or modify input file)
- dinodd (refinement step)

or dinomd
or dinoem

- rfacav (analysis - R-factors)

or rfacdg
or rfacgr
or rfacdis
or rfacpdb

- selpks (selection of NOE peaks)
- ananoe (analysis NOE trajectory)