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.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.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,($2+997.4787667132)*627.50956) }' > toplot.dat
xmgrace toplot.dat
[mjw99.mjw 16_1_25]$ 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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Received on Fri Dec 05 2008 - 14:17:53 PST
