Optaining IRMA

To optain IRMA please download the license agreement and mail or fax the signed form to:

Prof. Dr. R. Boelens
Department of NMR Spectroscopy - Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
Fax: +31 30 2537623
Email : boelens@nmr.chem.uu.nl

Installation

• 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 resulte 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

References:

• R. Boelens, T.M.G. Koning and R. Kaptein, "Determination of biomolecular structures from proton-proton NOE's using a relaxation matrix approach", J. Mol. Structure, 173 (1988) 299-311.
• R. Boelens, T.M.G. Koning, G.A. van der Marel, J.H. van Boom and R. Kaptein, "Iterative procedure for structure determination from proton-proton NOE's using a full relaxation matrix approach. Application to a DNA octamer", J. Magn. Reson., 82 (1989) 290-308.
• A.M.J.J. Bonvin, J.A.C. Rullmann, R.M.J.N. Lamerichs, R. Boelens and R. Kaptein "Ensemble Iterative Relaxation Matrix Approach: a new NMR refinement protocol applied to the solution structure of crambin." PROTEINS: Structure, Function & Genetics 15, 385-400 (1993).
• A.M.J.J. Bonvin, R. Boelens and R. Kaptein "Protein Structures: Relaxation matrix refinement." In: Encyclopedia of Nuclear Magnetic Resonance Vol. 6. Eds D.M. Grant and R.K. Harris, John Wiley & Sons, 3801-3811 (1996).