dacase / nabc

Nonperiodic force field calculations, with a "C" language interface rather than the original interface based on the Nucleic Acid Builder (NAB) molecular manipulation language
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Jargon-filled summary

This is conversion of AmberTool's NAB/SFF functionality, to keep the "SFF" part, but convert the "NAB" part to C. Optionally, one can also install the original NAB compiler.

More complete summary

The AmberTools package (https://ambermd.org) formerly contained a molecular maniupulation language, NAB (Nucleic Acid Builder, written primarily by Tom Macke) that interfaces to SFF (Simple Force Field, created originally by Dave Case).

The NAB language is expressive for some things, especially for short programs -- its original design was to serve as a "molecular AWK". But it doesn't scale well to larger projects, requires users to learn a new, C-like, language that isn't quite C, and doesn't do a good job of catching syntax errors at compile time.

The companion SFF library is written in C, and has a lot of nice features. It provides a lightweight code for carrying out simulations of non-periodic systems, and is file-compatible with the Amber package of programs.
All of the Amber generalized Born options are availabe, along with some unique (or at least, unusual) features, including:

This is an attempt to create driver programs in C that interface with SFF API. I have also included a slightly updated version of the NAB compiler itself, and the SHIFTS package for estimating NMR cheimcal shifts in proteins and nucleic acids (since it is built on top of NAB.) Right now it is a one-person (DAC) effort, but let me know if you would like to help out.

Primary Contributors

License

Mostly GPLv3; see the LICENSE file for full details.

How to install

Documentation

Reporting problems