MCM Molecular and Cellular Modeling
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HITS gGmbH (formerly EML Research gGmbH), Heidelberg

RAMD implementations from the MCM group at EML Research

  • AMBER8 (not maintained)

  • NAMD 2.6, 2.7 and 2.10

    The Random Acceleration Molecular Dynamics (RAMD) method can be used to carry out molecular dynamics simulations with an additional randomly oriented force applied to the center of mass of one molecule in the system. It can, for example, be used to identify egress routes for a ligand from a buried protein binding site.

    We initially implemented RAMD in the ARGOS program (Luedemann et al, 2000), and have subsequently implemented it in AMBER8 and NAMD. There are implementations by other groups in other codes (see below).

    RAMD and its applications (using the implementation in AMBER unless otherwise specified) are described in:

    • Luedemann, S.K., Lounnas, V. and R. C. Wade. How do Substrates Enter and Products Exit the Buried Active Site of Cytochrome P450cam ? 1. Random Expulsion Molecular Dynamics Investigation of Ligand Access Channels and Mechanisms. J Mol Biol, 303:797-811 (2000). doi:10.1002/jmbi.2000.4154 (First description of method and implementation in ARGOS)
    • Luedemann, S.K., Gabdoulline,R.R., Lounnas, V. and R. C. Wade. Substrate access to cytochrome P450cam investigated by molecular dynamics simulations: An interactive look at the underlying mechanisms. Internet Journal of Chemistry, 4, 6 (2001). (using the ARGOS implementation)
    • Winn,P., Luedemann, S.K., Gauges,R., Lounnas, V. and R. C. Wade. Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a new functional role for a buried arginine PNAS, 99, 5361-5366 (2002). Full text (using the ARGOS implementation)
    • Schleinkofer, K., Sudarko, Winn,P., Luedemann, S.K. and R. C. Wade. Do mammalian cytochrome P450s show multiple ligand access pathways and ligand channelling? EMBO Reports, 6, 584-589 (2005).doi:10.1038/sj.embor.7400420
    • Carlsson, P., Burendahl, S., Nilsson, L. Unbinding of retinoic acid from the retinoic acid receptor by random expulsion molecular dynamics. Biophys. J. 91, 3151-3161 (2006).doi:10.1529/biophysj.106.082917 (Implementation in CHARMM)
    • Wang, T., Duan, Y. Chromophore channeling in the G-protein coupled receptor rhodopsin. J. Am. Chem. Soc. 129, 6970-6971 (2007).doi:10.1021/ja0691977
    • Vashisth, H., Abrams, C.F. Ligand escape pathways and (un)binding free energy calculations for the hexameric insulin-phenol complex. Biophys. J. 95, 4193-4204 (2008).doi:10.1529/biophysj.108.139675 (Implementation for NAMD)
    • Long, D., Mu, Y. Yang, D. Molecular Dynamics Simulation of Ligand Dissociation from Liver Fatty Acid Binding Protein. PLoS ONE 4, e6801 (2008).doi:10.1371/journal.pone.0006081 (Implementation of a variant of RAMD in GROMACS)
    • Perakyla, M. Ligand unbinding pathways from the vitamin D receptor studied by molecular dynamics simulations. 38, 185-198 (2009).doi:10.1007/s00249-008-0369-x
    • Klvana, M. et al. Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored Using Classical and Random Acceleration Molecular Dynamics Simulations
      J. Mol. Biol. 392, 1339-1356 (2009).doi:10.1016/j.jmb.2009.06.076
    • Pavlova, M. et al. Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate Nature Chem. Biol. 5, 727-733 (2009).doi:10.1038/nchembio.205
    • Wang, T., Duan, Y. Ligand entry and exit pathways in the beta2-adrenergic receptor. J. Mol. Biol. 392, 1102-1115 (2009).doi:10.1016/j.jmb.2009.07.093

MCM software manager , December 2009

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