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From: Matthew Turner <TurnerM13.cardiff.ac.uk>

Date: Mon, 29 Oct 2018 22:35:09 +0000

Dear AMBER users,

I'm looking to calculate the angle between the planes of aromatic residues over a trajectory using cpptraj.

I've looked through the manual and the mailing list (particularly noting http://archive.ambermd.org/201512/0291.html) and found the commands needed:

vector name1 corrplane <mask1>

vector name2 corrplane <mask2>

vectormath vec1 name1 vec2 name2 dotangle out name1_name2_angle.dat

This calculates the vectors normal to the planes defined by <mask1> and <mask2> and then does the inverse cos of the dot product of those two vectors.

However, the results are not what I expected. I have selected a single frame pdb file (attached, zipped) and was looking at the interplane angle between His13 and His14 as a test case. In this frame, the residues sit nearly parallel - max 20 degrees out of parallel, by eye.

Using masks :13.CG,ND1,CD2,CE1,NE2 and :14.CG,ND1,CD2,CE1,NE2 to select the aromatic rings of His (rather than the whole residue) and running the above commands gives a dotangle value of 127.3200 degrees.

Firstly, this is clearly not correct, so where have I gone wrong? And secondly, shouldn't the angle between planes should be between 0 and 90 degrees (as simply explained here: https://youtu.be/C6ElQdRbHaE?t=287), or am I missing something? Calculating the dot product of name1 and name2 above gives -0.6063. If I was to take the modulus of that, arccos(0.6063) = 52 degrees, still not the near zero value I expected.

Any help appreciated!

Kind regards,

Matthew Turner

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Received on Mon Oct 29 2018 - 16:00:03 PDT

Date: Mon, 29 Oct 2018 22:35:09 +0000

Dear AMBER users,

I'm looking to calculate the angle between the planes of aromatic residues over a trajectory using cpptraj.

I've looked through the manual and the mailing list (particularly noting http://archive.ambermd.org/201512/0291.html) and found the commands needed:

vector name1 corrplane <mask1>

vector name2 corrplane <mask2>

vectormath vec1 name1 vec2 name2 dotangle out name1_name2_angle.dat

This calculates the vectors normal to the planes defined by <mask1> and <mask2> and then does the inverse cos of the dot product of those two vectors.

However, the results are not what I expected. I have selected a single frame pdb file (attached, zipped) and was looking at the interplane angle between His13 and His14 as a test case. In this frame, the residues sit nearly parallel - max 20 degrees out of parallel, by eye.

Using masks :13.CG,ND1,CD2,CE1,NE2 and :14.CG,ND1,CD2,CE1,NE2 to select the aromatic rings of His (rather than the whole residue) and running the above commands gives a dotangle value of 127.3200 degrees.

Firstly, this is clearly not correct, so where have I gone wrong? And secondly, shouldn't the angle between planes should be between 0 and 90 degrees (as simply explained here: https://youtu.be/C6ElQdRbHaE?t=287), or am I missing something? Calculating the dot product of name1 and name2 above gives -0.6063. If I was to take the modulus of that, arccos(0.6063) = 52 degrees, still not the near zero value I expected.

Any help appreciated!

Kind regards,

Matthew Turner

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AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

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