Software developed in our group

1. ComQum – a QM/MM interface
   [U. Ryde (1996) "The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum chemical and molecular mechanical calculations". J. Comput.-Aided Mol Design 10 , 153-164;
   U. Ryde & M. H. M. Olsson (2001) "Structure, strain, and reorganization energy of blue copper models in the protein". Intern. J. Quant. Chem., 81, 335-347.]
   
   
2. chargefit – a program to fit charges from QM calculations
   [E. Sigfridsson & U. Ryde (1998) "A comparison of methods for deriving atomic charges from the electrostatic potential and moments". J. Comp. Chem. 19, 377-395.]
   
   
3. ComQum-X – a program to combine QM/MM calculations and X-ray crystallographic refinement
   [U. Ryde, L. Olsen & K. Nilsson (2002) "Quantum chemical geometry optimisations in proteins using crystallographic raw data", J. Comp. Chem., 23, 1058-1070.]
   
   
4. Hess2FF – a program to obtain force-field parameters from QM calculations
   [K. Nilsson, D. Lecerof, E. Sigfridsson & U. Ryde (2003), "An automatic method to generate force-field parameters for hetero-compounds", Acta Crystallogr. D, 59, 274-289.]
   
   
5. Molcas – a general-purpose QM program. We have devloped the QM/MM code in this software (a variant of ComQum).
   http://www.teokem.lu.se/molcas/
   [G. Karlström, R Lindh, P.-Å. Malmqvist, B. O. Roos, U. Ryde, V. Veryazov, P.-O. Widmark, M. Cossi, B. Schimmelpfennig, P. Neogrady & L. Seijo (2003) "MOLCAS: a program package for computational chemistry", Comput. Materials Sci., 28, 222-239]
   
   
6. ComQum-NMR – a program to combine QM/MM calculations and NMR refinements
   [Y.-W. Hsiao, T. Drakenberg & U. Ryde (2005) "NMR structure determination of proteins supplemented by quantum chemical calculations: Detailed structure of the Ca2+ sites in the EGF34 fragment of protein S", J. Biomol. NMR, 31, 97-114].
   
   
7. calcqtcpfreee – a program to calculate QM/MM free energy differences (QTCP).
   [T. H. Rod & U. Ryde (2005) "Free energy barriers at the density functional theory level: methyl transfer catalyzed by catechol O-methyltransferase", J. Chem. Theory Comput., 1, 1240-1251].

8. EXAFS/QM – a program to combine QM calculations and EXAFS refinements
   [Y.-W. Hsiao, Y. Tao, J. E. Shokes, R. A. Scott, and U. Ryde (2006) "EXAFS structure refinement supplemented by computational chemistry", Inorg. Chem., submitted.

9. ComQum-EXAFS – a program to combine QM/MM calculations and EXAFS refinements (of whole proteins)
   [U. Ryde, Y.-W. Hsiao, L. Rulíšek, E. Solomon, Identification of the peroxy adduct in multi-copper oxidases by a combination of computational chemistry and EXAFS measurements, J. Am. Chem. Soc., submitted].