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Molecular Dynamics on Web Manual, v1.0 MDWeb Manual [ Table of Contents ] Table of Contents 1.- Introduction............................................................................................................................ 5 Motivation ............................................................................................................................................. 5 2.- Getting Started ....................................................................................................................... 7 MDWeb interface .................................................................................................................................. 7 User Registration ................................................................................................................................... 8 New Project ........................................................................................................................................... 8 3.- Structure Checking .............................................................................................................. 10 Choosing Structure Model................................................................................................................... 12 Choosing Structure Chain/s ................................................................................................................. 13 Choosing Atom/Residue Alternate Locations ..................................................................................... 13 Sequence Gaps/Non Consecutive Residues ........................................................................................ 14 Atom Clashes ...................................................................................................................................... 14 Improper Amide Assignment .............................................................................................................. 15 Improper Chirality ............................................................................................................................... 16 Unusual cis/trans Configuration .......................................................................................................... 16 Disulphide Bonds ................................................................................................................................ 17 Metals .................................................................................................................................................. 17 Structure containing DNA/RNA ......................................................................................................... 18 Residue Insertion ................................................................................................................................. 18 Ligands ................................................................................................................................................ 19 4.- Ligand Checking .................................................................................................................. 19 Atom name match window ................................................................................................................. 20 5.- Workspace ............................................................................................................................ 21 Structures ............................................................................................................................................. 22 Operations ........................................................................................................................................... 23 Services List ........................................................................................................................................ 23 Services Parameters ............................................................................................................................. 24 Visualization ........................................................................................................................................ 25 6.- MDWeb Operations ............................................................................................................. 26 Structure modification ......................................................................................................................... 27 Mutate Residue ............................................................................................................................... 27 Set-up for Simulation .......................................................................................................................... 27 Check for disulphide bonds ............................................................................................................ 27 Clean PDB ...................................................................................................................................... 27 Fix Side Chains ............................................................................................................................... 27 Add structural water molecules and ions ........................................................................................ 27 Set ionization state .......................................................................................................................... 28 Energy Minimization (Hydrogen Atoms) ............................................................................................ 28 2 MDWeb Manual [ Table of Contents ] NAMD ............................................................................................................................................ 28 GROMACS .................................................................................................................................... 28 Energy Minimization (All atoms) ....................................................................................................... 28 NAMD ............................................................................................................................................ 28 GROMACS ................................................................................................................................... 28 Solvate Structure ................................................................................................................................. 29 AMBER .......................................................................................................................................... 29 NAMD ............................................................................................................................................ 29 GROMACS .................................................................................................................................... 29 Molecular Dynamics simulations ....................................................................................................... 29 Simple Box Solvent System Equilibration (NPT, NVT, or NVE) .................................................. 29 Simple Box Solvent Molecular Dynamics (NPT, NVT, or NVE) .................................................. 30 NAMD - Amber ......................................................................................................................... 30 NAMD - Charmm ..................................................................................................................... 30 GROMACS ................................................................................................................................ 30 Coarse Grained Molecular Dynamics Simulations ............................................................................. 30 Coarse-Grained MD: Brownian Dynamics (C-Alpha) ................................................................... 30 Coarse-grained MD: DISCRETE dynamics (C-Alpha) ................................................................ 31 Coarse-grained MD: DISCRETE dynamics (Heavy atoms) .......................................................... 31 Coarse-grained MD: NMA (C-Alpha) ........................................................................................... 31 Molecular Dynamics Trajectory Simple Analysis ............................................................................... 32 Plot RMSd along the trajectory ...................................................................................................... 32 Plot RMSd x Residue ..................................................................................................................... 32 Plot BFactor per residue ................................................................................................................. 32 Plot Radius of Gyration along the trajectory .................................................................................. 33 Trajectory format conversions ............................................................................................................. 33 Compress trajectory to PCZ ........................................................................................................... 33 Decompress PCZ trajectory ........................................................................................................... 33 Convert trajectory to a set of PDB Files ........................................................................................ 34 Convert trajectory to BINPOS
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