The LARMD Server (Ligand and Receptor Molecular Dynamics) is a new online application for the user-friendly investigation of ligand-protein interactional binding mode based on conventional molecular dynamics (Int_mod) and dynamical unbinding process based on steered molecular dynamics simulations (Str_mod). It provides standard protocols to prepare structures, build force field libraries for molecules, detect tunnel, run unbiased and biased molecular dynamics simulations, calculate energy (MM/PBSA, decompose) and analyze trajectories, including Root-Mean-Square Deviation (RMSD), Radius of Gyration (Rg), Fraction of Native Contacts (Q), Root Mean Square Fluctuation (RMSF), B-factor, Principal Component Analysis (PCA), dynamic cross-correlations analysis, hydrogen bond analysis and so on. More important, normal mode analysis (Nor_mod) integrated is provided for conventional single protein without MD to visualize mode, analyze residue fluctuation, calculate deformation energy, and analyze protein structure network. At the same time, the information of submitted structure, linked to UniProt, also is provided.

1. PDB — Protein Data Bank.

1. Download the standard MOL2 file format introduction. MOL2.pdf
2. Download the standard PDB file format introduction. PDB.pdf