A versatile AMBER‐Gaussian QM/MM interface through PUPIL

The PUPIL package (Program for User Package Interfacing and Linking) originally was developed to interface different programs for multiscale calculations in materials sciences (Torras et al., J Comput Aided Mater Des 2006, 13, 201; Torras et al., Comput Phys Commun 2007, 177, 265). Here we present an extension of PUPIL to computational chemistry by interfacing two widely used computational chemistry programs: AMBER (molecular dynamics) and Gaussian (quantum chemistry). The benefit is to allow the application of the advanced MD techniques available in AMBER to a hybrid QM/MM system in which the forces and energy on the QM part can be computed by any of the methods available in Gaussian. To illustrate, we present two example applications: A MD calculation of alanine dipeptide in explicit water, and a use of the steered MD capabilities in AMBER to calculate the free energy of reaction for the dissociation of Angeli's salt. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008

[1]  D. Truhlar,et al.  QM/MM: what have we learned, where are we, and where do we go from here? , 2007 .

[2]  U. Singh,et al.  A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethers , 1986 .

[3]  Noam Bernstein,et al.  Spanning the continuum to quantum length scales in a dynamic simulation of brittle fracture , 1998 .

[4]  D. Wink,et al.  Neurotoxicity of nitroxyl: insights into HNO and NO biochemical imbalance. , 2005, Free radical biology & medicine.

[5]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[6]  Feliu Maseras,et al.  IMOMM: A new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states , 1995, J. Comput. Chem..

[7]  C. Brooks.  Computer simulation of liquids , 1989 .

[8]  G. Crooks.  Path-ensemble averages in systems driven far from equilibrium , 1999, cond-mat/9908420.

[9]  P. Naughton,et al.  Induction of Heme Oxygenase 1 by Nitrosative Stress , 2002, The Journal of Biological Chemistry.

[10]  Qiang Cui,et al.  Importance of van der Waals Interactions in QM/MM Simulations. , 2004, The journal of physical chemistry. B.

[11]  C. Jarzynski.  Nonequilibrium Equality for Free Energy Differences , 1996, cond-mat/9610209.

[12]  Thomas Frauenheim,et al.  Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment , 2001 .

[13]  H.-P. Cheng,et al.  PUPIL: A systematic approach to software integration in multi-scale simulations , 2007, Comput. Phys. Commun..

[14]  P. Kollman,et al.  Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation , 1993 .

[15]  S. C. Rogers,et al.  QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis , 2003 .

[16]  Markus Reiher,et al.  Atomistic Approaches in Modern Biology , 2007 .

[17]  D. Kass,et al.  Positive inotropic and lusitropic effects of HNO/NO− in failing hearts: Independence from β-adrenergic signaling , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[18]  H. Ohshima,et al.  Induction of DNA strand breakage and base oxidation by nitroxyl anion through hydroxyl radical production. , 1999, Free radical biology & medicine.

[19]  E. Kankuri,et al.  Nitric oxide-related species-induced protein oxidation: reversible, irreversible, and protective effects on enzyme function of papain. , 2005, Free radical biology & medicine.

[20]  Qiang Cui,et al.  Functional specificities of methylglyoxal synthase and triosephosphate isomerase: a combined QM/MM analysis. , 2002, Journal of the American Chemical Society.

[21]  Adrian E. Roitberg,et al.  Chapter 8 Nonequilibrium Approaches to Free Energy Calculations , 2005 .

[22]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[23]  M. Benaglia,et al.  Gazz. Chim. Ital , 1995 .

[24]  Weitao Yang,et al.  A density‐matrix divide‐and‐conquer approach for electronic structure calculations of large molecules , 1995 .

[25]  Bernard R. Brooks,et al.  Interfacing Q‐Chem and CHARMM to perform QM/MM reaction path calculations , 2007, J. Comput. Chem..

[26]  Emanuele Paci,et al.  Free energy for protein folding from nonequilibrium simulations using the Jarzynski equality. , 2006, The Journal of chemical physics.

[27]  Robert Q. Topper.  Atomistic Approaches in Modern Biology: From Quantum Chemistry to Molecular Simulations. Topics in Current Chemistry, Volume 268 Edited by Markus Reiher (ETH Zürich). Springer: Berlin, Heidelberg, New York. 2007. xii + 362 pp. $329.00. ISBN 978-3-540-38082-5. , 2007 .

[28]  P. Kollman,et al.  Automatic atom type and bond type perception in molecular mechanical calculations. , 2006, Journal of molecular graphics & modelling.

[29]  Per-Olov Löwdin,et al.  On the Nonorthogonality Problem , 1970 .

[30]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[31]  Erik Deumens,et al.  Software Integration in Multi-scale Simulations: the PUPIL System , 2006 .

[32]  Sándor Suhai,et al.  Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties , 1998 .

[33]  R. Widdop,et al.  Nitroxyl Anion Donor, Angeli’s Salt, Does Not Develop Tolerance in Rat Isolated Aortae , 2007, Hypertension.

[34]  H. Senn,et al.  QM/MM Methods for Biological Systems , 2006 .

[35]  R. S. Mulliken.  Electronic Population Analysis on LCAO–MO Molecular Wave Functions. I , 1955 .

[36]  V. Hornak,et al.  Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.

[37]  A. Roitberg,et al.  Free Energy Calculations with Non-Equilibrium Methods: Applications of the Jarzynski Relationship , 2006 .

[38]  Adrian J Mulholland,et al.  High-accuracy computation of reaction barriers in enzymes. , 2006, Angewandte Chemie.

[39]  K. Houk,et al.  Mechanisms of HNO and NO production from Angeli's salt: density functional and CBS-QB3 theory predictions. , 2004, Journal of the American Chemical Society.

[40]  T. Creighton.  Methods in Enzymology , 1968, The Yale Journal of Biology and Medicine.

[41]  P. Kollman,et al.  A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char , 1993 .

[42]  M. Karplus,et al.  A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations , 1990 .

[43]  P. Kollman,et al.  Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models , 1992 .

[44]  Thom Vreven,et al.  Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM. , 2006, Journal of chemical theory and computation.

[45]  Tai-Sung Lee,et al.  A pseudobond approach to combining quantum mechanical and molecular mechanical methods , 1999 .

[46]  A. English,et al.  Mass spectrometric analysis of nitroxyl-mediated protein modification: comparison of products formed with free and protein-based cysteines. , 2005, Biochemistry.

[47]  Ross C Walker,et al.  Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package. , 2007, The journal of physical chemistry. A.

[48]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.

[49]  J. Harvey,et al.  Spin-forbidden CO ligand recombination in myoglobin. , 2004, Faraday discussions.

[50]  M. Cuendet.  The Jarzynski identity derived from general Hamiltonian or non-Hamiltonian dynamics reproducing NVT or NPT ensembles. , 2006, The Journal of chemical physics.

[51]  M. N. Hughes,et al.  Synthesis, chemistry, and applications of nitroxyl ion releasers sodium trioxodinitrate or Angeli's salt and Piloty's acid. , 1999, Methods in enzymology.

[52]  David A. Dixon,et al.  Conformational Study of the Alanine Dipeptide at the MP2 and DFT Levels , 2002 .

[53]  C. Jarzynski,et al.  Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies , 2005, Nature.

[54]  Marc Albe,et al.  The dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials , 2000 .

[55]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..