[gmx-users] Converting between cartesian coordinates and torsion angles
Mark.Abraham at anu.edu.au
Fri Nov 12 17:35:08 CET 2010
On 13/11/2010 12:49 AM, Martin Kamp Jensen wrote:
> 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 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?
Section 4.2 has the relevant definitions. Table 5.5 pertains to the
definition of force field elements that act upon (for example) such
internal coordinates, which is not what you're looking for.
> I have included screenshots of Table 5.5 and the relevant part of
> some example .top file.
> (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.)
a) write something that post-processes the result of grompp -pp in
concert with the same coordinate file to get the internal coordinates, or
b) use a hacked version of mdrun that writes internal coordinates from
within src/gmxlib/bondfree.c (probably used as mdrun -rerun)
to create input for your procedure.
>  http://www.gromacs.org/@api/deki/files/126/=gromacs_manual-4.5.pdf
>  http://imada.sdu.dk/~mkjens04/gromacs/part_of_top_file.png
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