Citations
charmm_inps folder contains scripts and forcefields generated by CHARMM-GUI input generator (https://charmm-gui.org/?doc=input).
S. Jo, T. Kim, V.G. Iyer, and W. Im (2008) CHARMM-GUI: A Web-based Graphical User Interface for CHARMM. J. Comput. Chem. 29:1859-1865
B.R. Brooks, C.L. Brooks III, A.D. MacKerell, Jr., L. Nilsson, R.J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A.R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R.W. Pastor, C.B. Post, J.Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D.M. York, and M. Karplus (2009) CHARMM: The Biomolecular Simulation Program. J. Comput. Chem. 30:1545-1614
J. Lee, X. Cheng, J.M. Swails, M.S. Yeom, P.K. Eastman, J.A. Lemkul, S. Wei, J. Buckner, J.C. Jeong, Y. Qi, S. Jo, V.S. Pande, D.A. Case, C.L. Brooks III, A.D. MacKerell Jr, J.B. Klauda, and W. Im (2016) CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field. J. Chem. Theory Comput. 12:405-413
Jo, S., Song, K. C., Desaire, H., Mackerell, A. D., Jr., and Im, W. (2011) Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins. J. Comput. Chem. 32:3135-3141
S-J. Park, J. Lee, D.S. Patel, H. Ma, H.S. Lee, S. Jo, and W. Im (2017) Glycan Reader is Improved to Recognize Most Sugar Types and Chemical Modifications in the Protein Data Bank. Bioinformatics 33:3051-3057
S-J. Park, J. Lee, Y. Qi, N.R. Kern, H.S. Lee, S. Jo, IS Joung, K. Joo, J. Lee, and W. Im CHARMM-GUI Glycan Modeler for Modeling and Simulation of Carbohydrates and Glycoconjugates. Glycobiology 29:320-331
gromacs_mdps folder contains files generated by Galaxy | Comp Chem ZA Free energy Alchemical run tool (https://galaxy-compchem.ilifu.ac.za/).
Abraham, Mark James and Murtola, Teemu and Schulz, Roland and Páll, Szilárd and Smith, Jeremy C. and Hess, Berk and Lindahl, Erik (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. In SoftwareX, 1-2, pp. 19�25. [doi:10.1016/j.softx.2015.06.001]