The amber2accent script serves as a frontend for ptraj and is used to extract bond, angle and torsion parameters from MD snapshots. It defines the internal coordinates of a molecule in terms of the BAT-tree format described in: Killian et al., J. Chem. Phys. 127, 024107, (2007).

You can download the script here. This input, prmtop and trajectory files (of a solvated toluene, pdb here) serve as a simple test case.

Running the command ' input test.out' should produce this output file and several bond, angle and torsion files (N-1, N-2 and N-3, with N=15 in the test case), e.g. angle0011 or bond0005. The ptraj input file is also retained if you want to modify things by hand. All the values are collected and put into three lists, e.g. like this.

Running the script with the -h, -v or -sample switches provides some helpful hints.

For any questions and comments, please contact Thomas Steinbrecher at