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

Mark Abraham Mark.Abraham at anu.edu.au
Sun Oct 16 01:25:00 CEST 2011

On 16/10/2011 6:12 AM, Broadbent, Richard wrote:
> Have you thought about using the cross product. If you took the cross 
> product of the unit vector in the direction of every atom starting 
> from atom 1 then moved on to starting from atom 2 and so on you would 
> have a set of vectors normal to every group of three atoms. If you 
> then normalised them and defined one to be pointing upwards you could 
> then ensure using dot products that they all pointed the same way, a 
> condition like if a.b <0 b=-b would probably work you could then take 
> the mean of the vectors. This should give an average normal vector to 
> the plane of the molecule.
> If you're going to be doing this a lot I would suggest removing the 
> inherent double counting (r12=-r21).
> You could also think about weighting normal vectors in the averaging, 
> for instance you could do it based on the sine of the angle between 
> the vectors which generated them, or the mass of the atoms (H's will 
> more out of plane than carbons typically)

Calculating the principle axes of inertia is a better approach. There's 
a GROMACS tool that does it.


> Hope that's helpful
> Richard
> On 15/10/2011 15:45, "xiaodong huang" <xiaodonghuang2060 at gmail.com> wrote:
>     I send this message yesterday, but I myself donot see this
>     message, so, I send it again, very sorry for the spam.
>     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.
>     yours
>     xiaodong
>     school of chem, ANU
>     ------------------------------------------------------------------------

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