Search Results for "linux command" - Page 6

Plotamber is a Perl script for an easy and automated plotting of properties derived from molecular dynamics or minimization calculations done with Amber, NAMD or Charmm.

runsbml - Pathway Simulation Tool emulates the dynamics of biological pathways by calculating concentrations of biochemical compounds at different times and conditions.

CHIMP aims to provide a complete suite of tools for the investigation and modeling of chemical systems. It currently is able to parse chemical reaction mechanisms and run kinetic Monte Carlo simulations on the reacting system.

lazar (Lazy Structure-Activity Relationships) is a tool for the prediction of toxic activities of chemical structures.

MOLecular weight and atomic COMPosition calculator. Runs in simple command-line or web interface (as CGI). A visual Tk interface is planned.

The program fuses 2 sets of molecules. It tries different relative positions of molecules before binding them, so that there is no or minimal intersection in the resulting molecule. The atom to be fused in a molecule is labeled with an R symbol.

The platestats software aims to provide a convenient solution for analyzing the results of biological assays performed in 96- and 384-well plates.

md-utils is a set of command line tools written in C designed to perform certain operations and analysis on the molecular dynamics data. The supported operations involve trajectory coordinate transformation to the COM system, Cartesian coordinate transformation to selected internal coordinates and to projected normal mode coordinates, trajectory merging, selecting subsets of trajectory frames, selecting subsets of atoms, permuting atoms, etc. Analysis tools involve 1D, 2D and 3D data...