English
The software listed here is developed by Petr Kulhánek and his co-workers. The software with others not shown here are hosted on github.
CATs
CATs are Conversion and Analysis Tools. These tools are intended for manipulation and analysis of AMBER topology, coordinates, and trajectories. Operations can be performed on the whole structure or on a subset defined by a mask. CATs support parallel processing of AMBER trajectories together with management of obtained data. It also provides tools for simple virtual screening. Moreover, the package contains a scripting environment based on JavaScript, which opens ways for advanced analysis.
FFDevel
FFDevel is a suite of tools aimed at the force field development.
Infinity
Infinity is a software environment simplifying management of computational jobs. It consists of two subsystems: Advanced Module System (AMS), which manages scientific software, and Advanced Batch System (ABS), which is an extension of the PBSPro batch system.
Nemesis
Nemesis is an advanced molecular structure builder. It is able to build a molecule from predefined 3D fragments. Molecules can be visualized in several representations, including monoscopic and stereoscopic. The geometry of the built molecule can be easily measured and manipulated. Nemesis is a modular program, and its functionality can be extended by using various plugins. For example, it supports imports and exports of various chemical formats using the OpenBabel library. This library is also used for geometry optimization by several force fields.
PMFLib
PMFLib is a set of programs and libraries suited for free energy calculations by means of potential of mean force methods (PMF). It currently implements the following PMF methods: adaptive biasing method (ABF), constrained dynamics (CON), metadynamics (MTD), restrained dynamics (RST), and the string method (STM). The sampling can be improved by using the multiple walkers approach (MWA) in conjunction with the adaptive biasing method and metadynamics.