Dear Amber Community,
It is my pleasure to announce the availability of Wolf2Pack (www.wolf2pack.com) for use by the Amber community. Wolf2Pack is meant to serve as a platform for researchers to participate in the development of force-field parameters. This service can be used to test existing parameters, optimize missing parameters, or develop a stand-alone parameter set.
Wolf2Pack uses quantum mechanical (QM) potential energy curves as a target observable for parameter adjustment. In addition to this, Wolf2Pack provides wiki pages that outline each step in the parameterization process, examples for learning about the portal's usage and the optimization process, and a Message Board for community communication. We strongly encourage Wolf2Pack users to use the message board for asking questions, and for exchanging ideas related to force fields, parameters and their optimization.
An important part of Wolf2Pack is its molecular database. This database contains bond stretching, angle bending, and torsion rotational energy curves that are precomputed at several possible QM theory levels. Currently, there are approximately 150 molecules within this database, with new ones being added weekly. This number will rise to ~400 molecule in the next few months, with ~2,100 internal coordinates available for use.
Optimized and adjusted parameters are kept balanced (i.e. usable) with existing Amber force field by a) the use of existing Lennard-Jones parameters, b) proper use of nonbonded scaling factors (i.e. scee and scnb), and c) the development of resp partial atomic charges that are appropriate for the specified force field (i.e. QM theory levels and weighting factors).
Highlights include:
1. Parameters for closed-shell molecules composed of H, C, N, O, F, P, S, Cl, and Br,
2. Available Amber force fields: Parm99SB, Gaff, and Glycam06g-1,
3. Partial atomic charges are computed using the R.E.D. software,
4. Antechamber assigns the initial atom types, which can be adjusted by the user as desired,
5. Constraint molecular mechanics optimizations are performed via Sander,
6. QM calculations are performed using the GAMESS software, and
7. Available QM theories for constrained geometry optimization and relative potential energies: HF/6-31G(d), B3LYP/6-311++G(2d,2p), MP2/6-31++G(d,p), MP2/cc-pVDZ, and MP2/aug-cc-pVDZ.
Researchers can create a free account by visiting the portal and selecting "Create Account" link with in the Sign-In portlet. This account will give you access to the molecular database, perform constrained molecular mechanics minimizations, create new atom types, and adjust internal coordinate parameters.
Reasonable request can be made for the addition of new molecules, analogues thereof, and the QM calculations of a specific internal coordinate. I will do my best to add the requested data in a timely fashion. For more information behind Wolf2Pack's workflow, its philosophy, and the portal's usage - please see the first two references below.
Feedback is always welcomed. Obviously, there are many people who supported this project in various ways, for which I am grateful - including those who are developing Amber, R.E.D., and GAMESS.
Best Regards,
Dr. Karl N. Kirschner
Relevant references and websites:
Wolf2Pack:
1. D. Reith and K.N. Kirschner, A modern workflow for force-field development – Bridging quantum mechanics and atomistic computational models, Comput. Phys. Commun., 182 (2011) 2184-2191.
2. Ottmar Krämer-Fuhrmann, Jens Neisius, Niklas Gehlen, Dirk Reith, and Karl N. Kirschner, Wolf2Pack – Portal Based Atomistic Force-Field Development, J. Chem. Inf. Model., (2013) accepted. DOI: 10.1021/ci300290g
Amber9 (ambermd.org):
1. D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, K.M. Merz, D.A. Pearlman, M. Crowley, R.C. Walker, W. Zhang, B. Wang, S. Hayik, A. Roitberg, G. Seabra, K.F. Wong, F. Paesani, X. Wu, S. Brozell, V. Tsui, H. Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, P. Beroza, D.H. Mathews, C. Schafmeister, W.S. Ross, and P.A. Kollman (2006), AMBER 9, University of California, San Francisco.
R.E.D. (q4md-forcefieldtools.org/RED):
1. F.-Y. Dupradeau, A. Pigache, T. Zaffran, C. Savineau, R. Lelong, N. Grivel, D. Lelong, W. Rosanski and P. Cieplak, The R.E.D. tools: Advances in RESP and ESP charge derivation and force field library building, Phys. Chem. Chem. Phys., 12 (2011) 7821-7839.
GAMESS (www.msg.ameslab.gov/gamess):
1. Original Article M.W. Schmidt, K.K. Baldridge, J.A. Boatz, S.T. Elbert, M.S. Gordon, J.H. Jensen, S. Koseki, N. Matsunaga, K.A. Nguyen, S. Su, T.L. Windus, M. Dupuis, J.A. Montgomery, General Atomic and Molecular Electronic Structure System, J. Comput. Chem., 14 (1993) 1347-1363.
2. 2005 Update M.S. Gordon, M.W. Schmidt, Advances in electronic structure theory: GAMESS a decade later" in "Theory and Applications of Computational Chemistry: the first forty years" C.E. Dykstra, G. Frenking, K.S. Kim, G.E. Scuseria (editors), Elsevier, Amsterdam, 2005. (pp. 1167-1189).
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Karl N. Kirschner, Ph.D.
Fraunhofer-Institute for Algorithms
and Scientific Computing - SCAI
Department of Bioinformatics
53754 Sankt Augustin, Germany
Tel: +49 (0) 2241-14-2052
Fax: +49 (0) 2241-14-1328
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Received on Tue Apr 16 2013 - 02:30:02 PDT
