Hi, As far as I understand, a topology (a .top file) and a conformation (e.g., a .gro file) contain enough information to calculate the torsion angles of that specific conformation.
Table 5.5 (page 124) in the GROMACS manual[1] describes possible interactions (which are contained in the topology) between different molecules while the conformation contains the cartesian coordinates. I did not immediately find a way to convert between the cartesian coordinates and the torsion angles. Can GROMACS do it or do I need to understand (or just find) all the functions/formulas that are referenced in Table 5.5? I have included screenshots of Table 5.5[2] and the relevant part of some example .top file[3]. (Also, it seems that I can use the read_tpx method defined in include/tpxio.h to read in a topology from a .tpr file. This would then, after converting the cartesian coordinates of some conformation, enable me to work with the torsion angles in my own program before writing cartesian coordinates back for use with GROMACS.) Regards, Martin. [1] http://www.gromacs.org/@api/deki/files/126/=gromacs_manual-4.5.pdf [2] http://imada.sdu.dk/~mkjens04/gromacs/intra-molecular_interactions_definitions.png [3] http://imada.sdu.dk/~mkjens04/gromacs/part_of_top_file.png
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