[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.
Mark
>
> 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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