• To instal:
  Make

• To setup:
  alias irma source ~irma/irma2/cmmnds/irma

• To start:
  irma ---- directories and alias defined
  setup ---- define molecule name
  remind ---- show definitions and procedure
  

Before you start you have to create several files in your current directory. You need:

• the experimental NOEs in your NMR directory in the form of a result file of BUILDUP (named resmol.dat).
• a coordinate file in MD format with only protons (mol.mdh). If you have the all atom file, you must extract only the protons from this list. This file is needed to create the input file and is used in the procedure THENOES to create the relaxation matrix. If you want to calculate NOEs from several structures or from an MD trajectory, you can use the procedure THENOESAD. You need therefore and file containing the protons coordinates for all structures. This file can be created from GROMOS coordinates or trajectory file with the program CONVER.

Running IRMA2:

• First give the name of your molecule >
  
  setup == setup.csh
  
• Next define the input file for all IRMA programs >
  
  mxmat == matrix.csh
  
• Then start the IRMA procedure.
  The procedure is divided into three stages:
  
  • creation of theoretical NOE matrices on basis of the model >
    
    mxthe == thenoes.csh > thenoes.job created ( batch it)
    mxade == thenoesad.csh > thenoesad.job created ( batch it)
    
  • creation of the experimental NOE matrices >
    
    mxcre == crenoes.csh > mxcrex.job created ( run interactive)
    
  • merging of theory and experiment and calculation of new distances >
    
    mxmer == mergnoes.csh > mergnoes.job created ( batch it)
    

• Two additional procedures allow one to get the distances from the distances matrix and generate restraints files (mxrdis) and to calculate R-factors (mxrfac). The constraints are found on the file dismol.lis. This file can be used as input in restrained MD or DG calculations; the MD and DG programs should be obtained seperately.

Additional programs:

• mx2spn: calculate a NOE matrix with the 2spin approximation the result can be compared with the output of mx2dno in the procedure mxthe.
• mxspc2: calculate a spectrum on basis of a NOE matrix in the SMX format, the chemical shifts must be on the coordinate file
• assaro: stereospecific assignments for aromatic protons based on distances
• bitoas: conversion program for IRMA matrices binary <----> formatted