AMBER Archive (2008)

Subject: Re: AMBER: xLeap error

From: Mark Williamson (mjw_at_sdsc.edu)
Date: Mon Nov 10 2008 - 15:58:27 CST

Lili Peng wrote:
> Hi AMBER,
>
> I'm trying to build a molecule in xleap, but am getting the error:
> "Could not find angle parameter c3 - oh - c3". I'm pretty sure I
> generated the frcmod and prep files correctly. I'm attaching them in
> this email. Would you have any idea why the c3-oh-c3 angle is not found
> by xleap?
>
> Thanks,
> Lili

Hi,

The peg.frcmod file that you have attached is empty and the term
c3-oh-c3 is not in gaff.dat. Were you using say antechamber in a prior
step to generate a frcmod file with this missing parameter?

You need to obtain an equilibrium bond angle and associated force
constant for the angle term c3-oh-c3.

If I was facing this task, given from your prep file that the system is
quite small, I would carry out an optimisation using a high level QM
method and large basis set using a tool such as Gaussian. The final
structure from this would give you the equilibrium bond angle.

For the angle force constant, starting from this optimised structure, I
would use Gaussian's relaxed potential energy surface scan
(opt=modredundant with S code) say over an extension of 10 degrees with
1 degree steps. Be sure to use the same method and basis that you used
to get to this optimised structure for this process. Once you have these
10 points, you need to plot the energy difference from the original
optimised against angle extension. Be careful here since Gaussian's
energy output will be in Hartrees and extension in degrees but AMBER
will need these to be kcal and radians
(http://ambermd.org/formats.html#parm.dat section 5)

Next, you can then fit a quadratic function to them and the curvature of
this corresponds to the associated force constant.

As as quick example, I attach my Gaussian input files and some other
bits and bobs that I used when I was doing something similar for a small
organic molecule:

cat mg.com
%mem=7600MB
%nprocshared=2
#p opt=modredundant mp2/6-31g(d) geom=connectivity

Title Card Required

1 1
  C
  C 1 B1
  C 2 B2 1 A1
  C 2 B3 1 A2 3
       D1
  C 3 B4 2 A3 1
       D2
  H 3 B5 2 A4 1
       D3
  C 4 B6 2 A5 1
       D4
  H 4 B7 2 A6 1
       D5
  C 5 B8 3 A7 2
       D6
  H 5 B9 3 A8 2
       D7
  H 7 B10 4 A9 2
       D8
  H 9 B11 5 A10 3
       D9
  H 2 B12 1 A11 4
      D10
  C 1 B13 2 A12 4
      D11
  C 14 B14 1 A13 2
      D12
  C 14 B15 1 A14 2
      D13
  C 15 B16 14 A15 1
      D14
  H 15 B17 14 A16 1
      D15
  C 16 B18 14 A17 1
      D16
  C 19 B19 16 A18 14
      D17
  H 19 B20 16 A19 14
      D18
  H 20 B21 19 A20 16
      D19
  H 19 B22 16 A21 14
      D20
  C 1 B23 16 A22 14
      D21
  C 24 B24 1 A23 16
      D22
  C 24 B25 1 A24 16
      D23
  C 25 B26 24 A25 1
      D24
  C 26 B27 24 A26 1
      D25
  H 26 B28 24 A27 1
      D26
  C 27 B29 25 A28 24
      D27
  H 27 B30 25 A29 24
      D28
  H 30 B31 27 A30 25
      D29
  N 28 B32 26 A31 24
      D30
  N 17 B33 15 A32 14
      D31
  C 34 B34 17 A33 15
      D32
  H 35 B35 34 A34 17
      D33
  H 35 B36 34 A35 17
      D34
  H 35 B37 34 A36 17
      D35
  C 34 B38 17 A37 15
      D36
  H 39 B39 34 A38 17
      D37
  H 39 B40 34 A39 17
      D38
  H 39 B41 34 A40 17
      D39
  C 33 B42 28 A41 26
      D40
  H 43 B43 33 A42 28
      D41
  H 43 B44 33 A43 28
      D42
  H 43 B45 33 A44 28
      D43
  C 33 B46 28 A45 26
      D44
  H 47 B47 33 A46 28
      D45
  H 47 B48 33 A47 28
      D46
  H 47 B49 33 A48 28
      D47

    B1 1.46136900
    B2 1.41110202
    B3 1.41110175
    B4 1.39257943
    B5 1.08745181
    B6 1.39257825
    B7 1.08745271
    B8 1.39869263
    B9 1.08701531
    B10 1.08701565
    B11 1.08710300
    B12 2.63759333
    B13 2.47978570
    B14 1.37613629
    B15 1.42346650
    B16 1.42681876
    B17 1.08412404
    B18 1.42315422
    B19 1.37687697
    B20 1.08730496
    B21 1.08420240
    B22 2.59614736
    B23 2.48643001
    B24 1.42315434
    B25 1.37687776
    B26 1.42346753
    B27 1.42629308
    B28 1.08420275
    B29 1.37613641
    B30 1.08697914
    B31 1.08412356
    B32 1.35268563
    B33 1.35268560
    B34 1.46127943
    B35 1.08858384
    B36 1.09376473
    B37 1.09540312
    B38 1.46178798
    B39 1.09491410
    B40 1.08852763
    B41 1.09411824
    B42 1.46128023
    B43 1.09540274
    B44 1.08858325
    B45 1.09376540
    B46 1.46178743
    B47 1.08852847
    B48 1.09411811
    B49 1.09491337
    A1 120.34064110
    A2 120.34046292
    A3 120.07918774
    A4 119.45960139
    A5 120.07919372
    A6 119.45951154
    A7 120.22441424
    A8 119.78327963
    A9 119.78328704
    A10 119.97421564
    A11 76.62462474
    A12 92.65337579
    A13 150.95298237
    A14 29.46949551
    A15 121.09872604
    A16 118.60502898
    A17 117.25802199
    A18 121.55752106
    A19 119.07659853
    A20 118.64079533
    A21 79.06660100
    A22 95.42088024
    A23 29.18867294
    A24 150.74390402
    A25 117.25797112
    A26 121.03639885
    A27 118.64074602
    A28 121.50136259
    A29 119.19889406
    A30 118.60507979
    A31 121.28481875
    A32 121.22883808
    A33 120.38626684
    A34 108.66405467
    A35 110.71333138
    A36 111.38880238
    A37 120.38298509
    A38 111.20810949
    A39 108.65031927
    A40 110.89230848
    A41 120.38626765
    A42 111.38873098
    A43 108.66402477
    A44 110.71329943
    A45 120.38298342
    A46 108.65032873
    A47 110.89229452
    A48 111.20820861
    D1 180.00000000
    D2 179.29875625
    D3 2.42007421
    D4 179.29910076
    D5 2.42029161
    D6 1.40388552
    D7 -178.46775342
    D8 -178.46756490
    D9 179.29430976
    D10 -65.50095351
    D11 54.33998737
    D12 -158.36814518
    D13 -155.66745892
    D14 3.90408041
    D15 -175.12821352
    D16 179.26779035
    D17 0.18005316
    D18 -174.05432035
    D19 -175.99136169
    D20 124.33752403
    D21 -138.18991252
    D22 -155.58375804
    D23 -156.55398028
    D24 -179.26385113
    D25 2.38292498
    D26 -175.43609702
    D27 -2.26939386
    D28 -177.45678192
    D29 -176.68600069
    D30 178.74526755
    D31 179.18271102
    D32 177.49612892
    D33 -174.00813910
    D34 -55.20302209
    D35 66.49954475
    D36 -3.79328804
    D37 65.00934498
    D38 -175.69932070
    D39 -56.69670388
    D40 -3.03419463
    D41 66.49930011
    D42 -174.00838590
    D43 -55.20326017
    D44 175.67751357
    D45 -175.69878155
    D46 -56.69630808
    D47 65.00984176

  1 2 1.0 16 1.5 25 1.5
  2 3 1.5 4 1.5
  3 5 1.5 6 1.0
  4 7 1.5 8 1.0
  5 9 1.5 10 1.0
  6
  7 9 1.5 11 1.0
  8
  9 12 1.0
  10
  11
  12
  13 14 1.0
  14 15 2.0 16 1.5
  15 17 1.5 18 1.0
  16 19 1.5
  17 20 1.5 34 1.5
  18
  19 20 2.0 21 1.0
  20 22 1.0
  21
  22
  23 24 1.0
  24 25 1.5 26 2.0
  25 27 1.5
  26 28 1.5 29 1.0
  27 30 2.0 31 1.0
  28 30 1.5 33 1.5
  29
  30 32 1.0
  31
  32
  33 43 1.0 47 1.0
  34 35 1.0 39 1.0
  35 36 1.0 37 1.0 38 1.0
  36
  37
  38
  39 40 1.0 41 1.0 42 1.0
  40
  41
  42
  43 44 1.0 45 1.0 46 1.0
  44
  45
  46
  47 48 1.0 49 1.0 50 1.0
  48
  49
  50

A 16 1 25 S 5 1.0

(Output from gview)
[mjw99_at_mjw 16_1_25]$ cat scan.txt
         1.0000000000 -997.4787667706
         2.0000000000 -997.4787172349
         3.0000000000 -997.4785696224
         4.0000000000 -997.4783254787
         5.0000000000 -997.4779863344
         6.0000000000 -997.4775535294

[mjw99_at_mjw 16_1_25]$ cat scan_extract
#Exctracts bond scan data from the gview save file for the g03 calc

cat scan.txt | awk '{printf("%.10f %.10f\n",( ($1-1)*(6.283185/360)
)+0,($2+997.4787667132)*627.50956) }' > toplot.dat
xmgrace toplot.dat

[mjw99_at_mjw 16_1_25]$ cat toplot.dat
0.0000000000 -0.0000360191
0.0174532917 0.0310481062
0.0349065833 0.1236763612
0.0523598750 0.2768788670
0.0698131667 0.4896951574
0.0872664583 0.7612844325

Giving finally in my example case:

cd-c2-cd 100.211 121.085

regards,

Mark
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