AMBER-hub – Tools and information for AMBER and CPPTRAJ examples

AMBER and CPPTRAJ examples and recipes

A place created by users of the AMBER suite of biomolecular simulation programs to share, enrich and contribute to the learning and use of this tool. A computational chemist cookbook for recipes on how to use the codes provided in the AMBER tools package. We provide an easy-to-use place to learn the tool CPPTRAJ, the default package to perform analysis of trajectory information generated by the AMBER programs and force fields.

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CPPTRAJ introductory information to perform analysis

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CPPTRAJ Manual

CPPTRAJ description of actions, file formats and commands.

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CPPTRAJ cookbook

Collection of CPPTRAJ recipes and one-liners to perform analysis

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AMBER examples

Selected AMBER tutorials to perform molecular dynamics simulations

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Official AMBER

The official website for AMBER and AMBER-tools is located at ambermd.org
This website provides scripts, examples and tutorials based on day to day work form hard-core users of all the AMBER codes and programs. Please consider that this website is based on examples used in day to day research from a small comunity of people and should be regarded as starting points for personal research. We strive to expand the use of the AMBER programs and utilities and hence, support their use, although, we encourage common-sense in the examples provided here and erncourage that the users double check their results in orer to obtain meaningful results.