VMD-L Mailing List

From: chiessi_at_uniroma2.it
Date: Thu Jul 22 2021 - 05:55:17 CDT

Good morning

Working with this molecule (the coordinated in PDB format are at the
end of the message) I noticed that the value of some dihedral angles
is different depending on the method I used to measure it. I used:
a) the pick with mouse of the four atoms, that gives the value of the dihedral
b) the line command "measure dihed"

The results obtained with a) and b) methods are listed below for the
anomalous dihedrals:

Info) Added new Dihedrals label MOL1:O4/MOL1:C1/MOL1:O8/MOL1:C10 = -96.387154
measure dihed [[atomselect top "name O4 C1 O8 C10"] get index]
103.36381530761719

Info) Added new Dihedrals label MOL1:O15/MOL1:C13/MOL1:O20/MOL1:C22 =
-106.423363
measure dihed [[atomselect top "name O15 C13 O20 C22"] get index]
94.68035125732422

Info) Added new Dihedrals label MOL1:O9/MOL1:C7/MOL1:O14/MOL1:C16 =
-106.413147
measure dihed [[atomselect top "name O9 C7 O14 C16"] get index]
96.04247283935547

Info) Added new Dihedrals label MOL1:C10/MOL1:O8/MOL1:C1/MOL1:C2 = 143.676331
measure dihed [[atomselect top "name C10 O8 C1 C2"] get index]
-38.713417053222656

By inspecting the molecule it is evident that the right value is that
obtained with a).

However, I would like to understand if I am wrong in something when
using "measure dihed". For many other dihedral angles in this molecule
I get the same value with a) and b) methods.

Thanks for any suggestion

Ester

__________________

TITLE Grunge ROck MAChoS
MODEL 1
ATOM 1 C1 MOL 1 -6.016 -0.209 -0.093 0.298667.00
        C
ATOM 2 O4 MOL 1 -6.490 1.115 0.205 -0.546499.00
        O
ATOM 3 O8 MOL 1 -4.796 -0.367 0.552 -0.395148.00
        O
ATOM 4 C10 MOL 1 -3.593 -0.134 -0.198 0.087925.00
        C
ATOM 5 C9 MOL 1 -3.133 1.316 0.016 0.042422.00
        C
ATOM 6 C8 MOL 1 -1.713 1.534 -0.515 0.318595.00
        C
ATOM 7 C7 MOL 1 -0.779 0.436 0.030 0.257354.00
        C
ATOM 8 O9 MOL 1 -1.289 -0.839 -0.320 -0.443242.00
        O
ATOM 9 C11 MOL 1 -2.551 -1.143 0.292 0.042531.00
        C
ATOM 10 C12 MOL 1 -2.870 -2.639 -0.043 0.875354.00
        C
ATOM 11 O10 MOL 1 -3.967 -2.883 -0.632 -0.825435.00
        O
ATOM 12 O11 MOL 1 -1.995 -3.460 0.299 -0.825435.00
        O
ATOM 13 H23 MOL 1 -2.458 -1.054 1.388 0.066513.00
        H
ATOM 14 O14 MOL 1 0.479 0.573 -0.565 -0.488503.00
        O
ATOM 15 C16 MOL 1 1.646 0.491 0.254 0.205766.00
        C
ATOM 16 C15 MOL 1 2.254 -0.917 0.246 0.251145.00
        C
ATOM 17 C14 MOL 1 3.669 -0.913 0.833 0.023633.00
        C
ATOM 18 C13 MOL 1 4.535 0.106 0.099 0.201172.00
        C
ATOM 19 O15 MOL 1 3.941 1.391 0.254 -0.331659.00
        O
ATOM 20 C17 MOL 1 2.641 1.517 -0.338 -0.035713.00
        C
ATOM 21 C18 MOL 1 2.218 2.961 -0.075 0.213947.00
        C
ATOM 22 O16 MOL 1 2.202 3.254 1.319 -0.695593.00
        O
ATOM 23 H30 MOL 1 3.082 3.006 1.653 0.429254.00
        H
ATOM 24 H10 MOL 1 1.202 3.118 -0.443 0.045148.00
        H
ATOM 25 H11 MOL 1 2.906 3.630 -0.612 0.045148.00
        H
ATOM 26 H27 MOL 1 2.703 1.347 -1.424 0.095652.00
        H
ATOM 27 O20 MOL 1 5.799 0.146 0.678 -0.388791.00
        O
ATOM 28 C22 MOL 1 6.928 0.170 -0.211 0.028042.00
        C
ATOM 29 C21 MOL 1 7.436 -1.265 -0.414 0.245591.00
        C
ATOM 30 C20 MOL 1 8.735 -1.246 -1.217 0.164784.00
        C
ATOM 31 C19 MOL 1 9.749 -0.314 -0.525 0.091943.00
        C
ATOM 32 O17 MOL 1 10.142 -0.934 0.674 -0.40459.00 O
ATOM 33 C26 MOL 1 11.241 -0.295 1.322 -0.044241.00
        C
ATOM 34 H41 MOL 1 11.474 -0.893 2.205 0.092539.00
        H
ATOM 35 H42 MOL 1 10.988 0.726 1.628 0.092539.00
        H
ATOM 36 H43 MOL 1 12.119 -0.263 0.662 0.092539.00
        H
ATOM 37 O21 MOL 1 9.221 0.985 -0.332 -0.453004.00
        O
ATOM 38 C23 MOL 1 8.008 1.050 0.441 0.305403.00
        C
ATOM 39 C24 MOL 1 7.613 2.516 0.523 -0.39280.00 C
ATOM 40 H14 MOL 1 6.675 2.621 1.074 0.107484.00
        H
ATOM 41 H15 MOL 1 7.476 2.930 -0.483 0.107484.00
        H
ATOM 42 H16 MOL 1 8.390 3.094 1.033 0.107484.00
        H
ATOM 43 H35 MOL 1 8.201 0.659 1.450 0.086243.00
        H
ATOM 44 H12 MOL 1 10.621 -0.154 -1.176 0.172951.00
        H
ATOM 45 O18 MOL 1 8.443 -0.768 -2.526 -0.682910.00
        O
ATOM 46 H31 MOL 1 9.247 -0.858 -3.062 0.45668.00 H
ATOM 47 H13 MOL 1 9.155 -2.260 -1.254 0.088685.00
        H
ATOM 48 O19 MOL 1 6.484 -2.086 -1.073 -0.688366.00
        O
ATOM 49 H32 MOL 1 5.757 -2.264 -0.441 0.425346.00
        H
ATOM 50 H36 MOL 1 7.674 -1.674 0.579 0.042562.00
        H
ATOM 51 H37 MOL 1 6.638 0.600 -1.176 0.158716.00
        H
ATOM 52 H34 MOL 1 4.598 -0.148 -0.969 0.11912.00 H
ATOM 53 O12 MOL 1 4.259 -2.205 0.710 -0.623962.00
        O
ATOM 54 H28 MOL 1 3.540 -2.848 0.852 0.437287.00
        H
ATOM 55 H33 MOL 1 3.634 -0.615 1.893 0.116235.00
        H
ATOM 56 O13 MOL 1 1.469 -1.910 0.904 -0.67336.00 O
ATOM 57 H29 MOL 1 1.326 -1.626 1.824 0.437362.00
        H
ATOM 58 H26 MOL 1 2.312 -1.256 -0.795 0.106824.00
        H
ATOM 59 H9 MOL 1 1.410 0.793 1.283 0.068972.00
        H
ATOM 60 H7 MOL 1 -0.699 0.519 1.128 0.094327.00
        H
ATOM 61 O6 MOL 1 -1.230 2.842 -0.233 -0.673471.00
        O
ATOM 62 H24 MOL 1 -1.274 2.981 0.729 0.444322.00
        H
ATOM 63 H21 MOL 1 -1.716 1.451 -1.607 0.112573.00
        H
ATOM 64 O7 MOL 1 -3.998 2.245 -0.621 -0.718937.00
        O
ATOM 65 H25 MOL 1 -4.896 2.085 -0.267 0.48174.00 H
ATOM 66 H22 MOL 1 -3.119 1.493 1.107 0.083692.00
        H
ATOM 67 H8 MOL 1 -3.784 -0.305 -1.263 0.105353.00
        H
ATOM 68 H1 MOL 1 -5.907 -0.316 -1.183 0.095651.00
        H
ATOM 69 C2 MOL 1 -6.974 -1.276 0.447 0.066474.00
        C
ATOM 70 O1 MOL 1 -6.573 -2.556 0.003 -0.621853.00
        O
ATOM 71 H18 MOL 1 -5.582 -2.588 -0.074 0.402987.00
        H
ATOM 72 H17 MOL 1 -6.947 -1.201 1.547 0.099043.00
        H
ATOM 73 C3 MOL 1 -8.418 -1.020 -0.011 0.119218.00
        C
ATOM 74 O2 MOL 1 -9.334 -1.843 0.704 -0.437022.00
        O
ATOM 75 C25 MOL 1 -9.668 -3.069 0.066 0.116232.00
        C
ATOM 76 H38 MOL 1 -10.421 -3.552 0.694 0.038712.00
        H
ATOM 77 H39 MOL 1 -8.798 -3.727 -0.034 0.038712.00
        H
ATOM 78 H40 MOL 1 -10.098 -2.894 -0.932 0.038712.00
        H
ATOM 79 H2 MOL 1 -8.485 -1.234 -1.089 0.099146.00
        H
ATOM 80 C4 MOL 1 -8.834 0.437 0.207 0.20254.00 C
ATOM 81 O3 MOL 1 -10.090 0.636 -0.428 -0.715397.00
        O
ATOM 82 H19 MOL 1 -10.232 1.604 -0.430 0.439005.00
        H
ATOM 83 H3 MOL 1 -8.909 0.616 1.293 0.058444.00
        H
ATOM 84 C5 MOL 1 -7.773 1.398 -0.365 0.229691.00
        C
ATOM 85 H4 MOL 1 -7.738 1.271 -1.459 0.036496.00
        H
ATOM 86 C6 MOL 1 -8.056 2.868 -0.027 0.203684.00
        C
ATOM 87 H5 MOL 1 -7.252 3.500 -0.422 0.054588.00
        H
ATOM 88 H6 MOL 1 -8.084 2.989 1.060 0.054588.00
        H
ATOM 89 O5 MOL 1 -9.334 3.300 -0.510 -0.704953.00
        O
ATOM 90 H20 MOL 1 -9.262 3.438 -1.469 0.45311.00 H
TER
ENDMDL 

-- 
Ester Chiessi
Department of Chemical Sciences and Technologies
University of Rome Tor Vergata
Via della Ricerca Scientifica
00133 Rome (Italy)
E-mail: ester.chiessi_at_uniroma2.it
tel +39 6 72594462
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