[AMBER] Wrong Angel Given by Cpptraj?

From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Date: Fri, 29 Oct 2021 06:38:16 -0400

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

vectormath vec1 His1 vec2 His2 dotangle out HisHisAng1283test.dat name HisHisAng1283


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Received on Fri Oct 29 2021 - 04:00:03 PDT
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