[gmx-users] how to calculate the normal of plane for Tryptophan or how to get the comparison matrix in g_rms

xiaodong huang xiaodonghuang2060 at gmail.com
Sat Oct 15 05:43:38 CEST 2011

Dear gmxer's
I am simulating a protein, want to calculate the normal of plane for
Tryptophan residue amino acid in that protein.
We need to take into account that, in simulation, atoms of TRP vibrate all
the time, and they are not always on the same plane:
If they were on the same plane in my simulation, to calculate the normal
would be rather straighforward.
As those atoms are not on the same plane, I think my calculation should be
something like least square fitting. I look at g_rms command,
and plan to calculate the normal in following steps:
1. create a Tryptophan with ideal configuration, where all 8 C atom and N
atom (except CB atom) should be in the same plane,
    I put these 9 atoms in xy plane, and the normal of this TRP molecule is
just z axis
2.I then calculate the rms between the TRP residue in my simulation and that
ideal TRP molecule
3.If I know the rotate matrix (e.g. how to rotate the TRP in my simulation
in the least-squares fitting of rms calculation), then I
   just rotate z axis (0,0,1) back ( in other words, multiple z axis (0,0,1)
with the inverse of that rotate matrix) to get the plane normal
   for TRP in my simulation.
So, I am wondering how to know the the rotate matrix when g_rms do the
least-squares fitting? Is that in the comparison matrix
dumped by the -bin option? If so, how to read the rotate matrix from that
binary file produced by -bin option?
Or, if there is other way that I can calculate plane normal for TRP?
Thank you so much for your kind help.
school of chem, ANU
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