Re: [AMBER] Problem measuring angle in CPPTRAJ

From: Daniel Roe <>
Date: Mon, 1 Nov 2021 10:05:01 -0400


Sorry for the delay in responding. I've been out with an illness for a while.

One thing to keep in mind with 'corrplane' vectors is that there are
*two* vectors that can be perpendicular to the plane passing through a
group of atoms; they point in opposite directions. So I'm guessing
what is happening here is that your 'corrplane' vector is pointing in
the opposite direction, which is why you're getting an angle greater
than 90 deg. One way to visualize this is to write out and view the
vector pseudo-trajectory:

vector V1 corrplane :1283&.CG1,ND11,CD21,NE21,CD11
# Write vector pseudo trajectory in mol2 format
writedata vector.mol2 vectraj trajfmt mol2 V1

You can correct for vectors that point the opposite way you expect by
calculating 180-X for each value X that is greater than 90 degrees.

Hope this helps,


On Sat, Oct 30, 2021 at 4:14 PM Matthew Guberman-Pfeffer
<> wrote:
> Dear Amber Community,
> I am using the below CPPTRAJ script to measure the angle between the planes of imidazole side chains coordinated to the iron center of heme groups. For the attached structure, I get angles within 1.5° of the reported values for five of the six hemes (residue IDs 1280, 1274, 1277, 1271, and 1268), but for the sixth one (res ID 1283), I get an angle that is ~100° instead of the reported ~79°. I measured the angle with a different program (Maestro of the Schrodinger Suite), and found the angle to be 79°. I am wondering if you can please help me understand why I am getting a wrong angle for the pair of imidazoles in resid 1283, but not resid 1280, 1274, etc.? Just so it is clear, the attached structure is the as-prepared-with-tleap CryoEM structure, with everything but the hemes of interest stripped off because of the limit on the size of postings to the list.
> parm OnlyHemes.pdb
> trajin OnlyHemes.pdb
> vector His1 corrplane :1283&.CG1,ND11,CD21,NE21,CD11
> vector His2 corrplane :1283&.CG2,ND12,CD22,NE22,CE12
> run
> vectormath vec1 His1 vec2 His2 dotangle out HisHisAng1283test.dat name HisHisAng1283
> run
> Best,
> Matthew
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Received on Mon Nov 01 2021 - 07:30:02 PDT
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