Computational protocol: Optimal Identification of Semi Rigid Domains in Macromolecules from Molecular Dynamics Simulation

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Protocol publication

[…] To demonstrate the performance and usefulness of the method we have applied it to a series of molecular systems:A MD trajectory of Ala, containing solute atoms.A MD trajectory of the artificial peptide MR121-GSGSW (i.e. a chromophore MR121 is connected with GLY-SER-GLY-SER-TRP), containing solute atoms. MD trajectories of the wild type of transthyretin (PDB ID code, 1DVQ) , containing solute atoms, and two point variants 58Arg, 58His, containing and solute atoms respectively. The point mutants were generated by Modeller Release 9v5 .A MD trajectory of the chaperone GroEL-GroES (PDB ID code, 1GRU), containing solute atoms.All molecular dynamics trajectories were generated by the molecular dynamics package Gromacs 3.3 using the standard distribution force field GROMOS96 43a2. The solutes were solvated in SPC216 water in a cubic box with at least of water on each side of the solute. The structures were equilibrated with a molecular dynamics simulation constraints on all bonds of the protein. A subsequent energy minimisation without position restraints was performed with a steepest descent minimization. The production runs were done with LINCS constraints on the hydrogen bond length and a time step, the trajectory was written every . The electrostatic interactions were computed using the smooth Particle Mesh Ewald algorithm (PME), where the full direct and reciprocal space parts were calculated each step with a lattice spacing of . The Van der Waals interactions were computed with a cut-off at . All simulations were performed with Berendsen temperature coupling and isotropic pressure coupling to . The temperatures used were for systems and for systems . […]

Pipeline specifications

Software tools MODELLER, GROMACS, P-LINCS
Application Protein structure analysis