Similar protocols

Pipeline publication

[…] th its recent extension to carbohydrates [] in combination with ParamChem (http:/www.paramchem.org) and the CHARMM generalized force field (CGenFF) []. This force field has been already tested in a large variety of systems and found very reliable in reproducing several biophysical properties, including also the folding process of proteins [] where it was shown to provide results very similar to other popular force fields (several versions of AMBER and modifications of CHARMM) in the characterization of the native state of proteins. The van der Waals forces were cut off at 1.2nm while PME was used for long range electrostatic interactions with a grid spacing of 1Å. After energy minimization (NAMD’s conjugate gradient algorithm, 15000 steps) of hydrogen atoms and water molecules, the system was heated and equilibrated for 10ns. Production runs statistics are given in . We employed collective variable constraints (distanceXY, directiondir or orient) to keep the main axis of the molecule aligned to the simulation box and verified that this had no influence on the overall dynamics by comparing to unconstrained simulations., To identify the collective motions of the whole Fg molecule and of its subdomains we performed several principal component analyses (PCA) [] using wordom [] and GROMACS utilities []. DynDom [] was used to identify rigid domains and hinges of motion. The overlap between spaces spanned by the dominant PCA modes of different simulations was used to quantify the similarity of the observed dynamics []. The overlap is defined as: O({x_i},{y_i})=1n∑i=1n∑j=1n(x_i·y_j)2,(3) where {x¯i} and {y¯j} are the two subspaces spanned by the principle components x¯1…x¯n and y¯1…y¯n, respectively., The linear correlation coefficient between two variables is defined as the ratio between the covariance of the two variables and the product of the two standard deviations, r=∑(xi−x‾)(yi−y‾)/∑(xi−x‾)2(yi−y‾)2. If P 1(t), P 2(t), P N(t) are the projections of the trajectory at time t along the 1st […]

Pipeline specifications

Software tools NAMD, Wordom, GROMACS, DynDom