[gmx-users] Converting between cartesian coordinates and torsion angles

Martin Kamp Jensen martin.kamp.jensen at gmail.com
Fri Nov 12 14:49:21 CET 2010


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.)


[1] http://www.gromacs.org/@api/deki/files/126/=gromacs_manual-4.5.pdf
[3] http://imada.sdu.dk/~mkjens04/gromacs/part_of_top_file.png
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