… Amber and AmberTools form a collection of programs that are designed to work together to
facilitate system setup, MD simulations, and trajectory analysis for biomolecules. It is useful to …

… of Amber and, by association, AmberTools including only a brief description of the new … in
Ambertools and Amber Forcefields we briefly outline the new additions to AmberTools and the …

Molecular dynamics (MD) simulations of explicit representations of fluorescent dyes
attached via a linker to a protein allow, eg, probing commonly used approximations for dye …

… This section provides a list of the main programs included with AmberTools. Each program
included in the suite is listed here with a very brief description of its main function along with a …

… the combination of AmberTools and Amber itself. We expect that AmberTools will be dynamic…
We hope to add new functionality to AmberTools as additional programs become available. …

The expulsion of water from surfaces upon molecular recognition and nonspecific association
makes a major contribution to the free energy changes of these processes. In order to …

… other programs as well, including the NAB programming environment in AmberTools. … tory,
and is described in Chapter 2 of the AmberTools manual. It contains topology for the standard …

… To the best of our knowledge, the current version of MCPB or MCPB.py in AmberTools and
the Hess2FF program do not have this flexible option yet and support only a limited number …

… The original Amber and AmberTools software packages have to be obtained and installed
… 16þ and AmberTools v.17þ (ie the older versions of AmberTools do not include the FF15IPQ …

As part of our ongoing efforts to support diverse force fields and simulation programs in
CHARMM-GUI, this work presents the development of FF-Converter to prepare Amber simulation …