VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jul 22 2021 - 07:41:39 CDT

Ester,

The problem is that when making an atom selection the order of atoms is
always the order in which they are stored internally, but for computing the
dihedral angle the order matters. Thus if the order of atoms matches the
one you use when manually selecting atoms (or is compatible by symmetry)
you get consistent numbers, otherwise not.

Thus your way of calling measure is not correct.

Axel 

--
Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!o5z-HxJg8ldCaHPVAVY3ypx27UpL9KEu6U3UA6qhhpGt21yqdZMjUIAjX33L0X3Pnw$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste, Italy
On Thu, Jul 22, 2021, 07:28 <chiessi_at_uniroma2.it> wrote:
> 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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