Version 7c, December 2005

J. García de la Torre, M.L. Huertas y B. Carrasco. "HYDRONMR: Prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations", Journal of Magnetic Resonance B, 138-146 (2000).

HYDRONMR is a computer program intended for the calculation of NMR relaxation of small, quasirigid macromolecules whose structure, with atomic resolution, is taken from a PDB file of atomic coordintes. For this purpose, the basic hydrodynamic quantities that are involved in dynamic NMR are evaluated in the same fashion as in the closely related HYDROPRO program. Then, HYDRONMR calculates NMR quantities like T1, T2, NOE, etc. for each residue of a globular protein (the 15N-H and 13Ca -H vectors are calculated by the program itself. Alternatively, an user-supplied list of vectors can be given. HYDRONMR also reports the translational diffusion coefficient, which is available, among other sources, from some NMR experiments.

If the computing time needed for the HYDRONMR calculation (2-3 minutes) is too long for your purposes, we provide another program, Fast-HYDRONMR which is externally identical program. Internally, this program employs an approximate procedure for the calculation of the diffusion tensor. The bias introduced for the approximation is, hopefully, not much larger than other computational or experimental errors. The main advantage is that Fast-HYDRONMR calculation is much faster, with CPU time of a few seconds.

For more details, see the HYDRONMR and HYDRONMR User Guide

Files for download:

hydronmr.pdf PDF Paper on HYDRONMR
hydronmr7c.pdf PDF User Guide
hydronmr7cmsd.exe Executable MS DOS/Windows
hydronmr7c2lnx.exe Executable Linux
hydronmr.dat ASCII Sample of main input file
6lyz.pdb ASCII Sample of coordinates file
lysozyme31-nmr.res ASCII General results
lysozyme31-nmr.t12 ASCII Results for T1/T2
lysozyme31-nmr-pri.bea ASCII (PDB) Primary model, RasMol
lysozyme31-nmr-pri.vrml ASCII (VRML) Primary model, VRML-Cortona
fast-hydronmr-1.pdf PDF Paper on Fast-HYDRONMR
fast-hydronmr-2.pdf PDF Appendix to Paper on Fast-HYDRONMR
fast-hydronmr7cmsd.exe Executable MS DOS/Windows
fast-hydronmr7c2lnx.exe Executable Linux
lysozyme31-fast-nmr.res ASCII General results
lysozyme31-fast-nmr.t12 ASCII Results for T1/T2

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