Dear Amber experts,
I would appreciate very much your help with the following:
I have a question about antechamber and frcmod file. We have run the molecule bellow through antechamber, and obtained the frcmod attached. The molecule in mol2 file also attached. We have carefully looked at all the DIHE and IMPROPER comments.
We have found that the DIHE refers to the propyl ring atoms, for which I understand there are not parameters with regards to their specific environment in this molecule, is that correct?
If so, how should we set those DIHE angle parameters? Using gamess?
What is the best alternative to do it without gamess / gaussian?
We obtained this geometry by building the molecule with ChemAxon MarvinSketch software.
Additionally, I understand the IMPROPER list relates to the planar dihedral angles, for which the default is 180 degrees; we have again checked carefully and found that there was one incorrect angle:
c3-c3-nh-ca 1.1 180.0 2.0
Which we measured and found it should be 125 instead of 180 (this is an aliphatic ring), that I understand was mistaken to be aromatic, is that correct?
Finally, we don’t understand the following dihedral definition:
c -c -cd-cc 1.1 180.0 2.0 Using the default value
This should be the C7, C8, C9 (cc, cd, c respectively) atoms, but I cannot find the other c-, how is this dihedral defined?
Thanks a lot, and sorry for so many questions,
Fabian
Remark line goes here
MASS
BOND
ANGLE
DIHE
cx-cx-na-ca 6 0.000 0.000 2.000 same as X -c3-na-X , penalty score= 92.0
h1-cx-na-ca 6 0.000 0.000 2.000 same as X -c3-na-X , penalty score= 92.0
cx-cx-na-cc 6 0.000 0.000 2.000 same as X -c3-na-X , penalty score= 92.0
h1-cx-na-cc 6 0.000 0.000 2.000 same as X -c3-na-X , penalty score= 92.0
IMPROPER
ca-ca-ca-nh 1.1 180.0 2.0 Using the default value
ca-ca-ca-ha 1.1 180.0 2.0 Using general improper torsional angle X- X-ca-ha, penalty score= 6.0)
ca-ca-ca-na 1.1 180.0 2.0 Using the default value
c -ca-ca-ca 1.1 180.0 2.0 Using the default value
ca-cc-na-cx 1.1 180.0 2.0 Same as c2-c2-na-c3, penalty score= 70.7)
cd-h4-cc-na 1.1 180.0 2.0 Same as X -X -ca-ha, penalty score= 67.2 (use general term))
c -c -cd-cc 1.1 180.0 2.0 Using the default value
ca-cd-c -o 10.5 180.0 2.0 Using general improper torsional angle X- X- c- o, penalty score= 6.0)
c3-c3-nh-ca 1.1 125.0 2.0 Using the default value
cd-o -c -o 1.1 180.0 2.0 Using general improper torsional angle X- o- c- o, penalty score= 3.0)
NONBON
.<TRIPOS>MOLECULE
MOL
93 98 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 C1 -18.3440 44.5650 -13.2320 ca 1 MOL 0.032900
2 C2 -18.1060 45.6930 -14.1520 ca 1 MOL 0.127600
3 C3 -19.1400 46.1860 -15.0420 ca 1 MOL -0.243000
4 C4 -20.4180 45.5660 -15.0310 ca 1 MOL 0.212600
5 C5 -20.6720 44.4950 -14.1050 ca 1 MOL -0.209600
6 C6 -19.6630 43.9820 -13.2290 ca 1 MOL -0.067000
7 N1 -21.4180 45.9880 -15.8890 na 1 MOL -0.512800
8 C7 -22.6830 45.4760 -15.7900 cc 1 MOL 0.063000
9 C8 -23.0220 44.4410 -14.8970 cd 1 MOL -0.260400
10 C9 -21.9840 43.9450 -14.0690 c 1 MOL 0.599900
11 O1 -22.2450 43.0030 -13.2820 o 1 MOL -0.549100
12 F1 -17.4130 44.1140 -12.4380 f 1 MOL -0.153900
13 N2 -16.8670 46.3770 -14.2730 nh 1 MOL -0.620000
14 C10 -15.7550 46.1170 -13.3890 c3 1 MOL 0.181800
15 C11 -15.2810 47.4390 -12.7390 c3 1 MOL 0.130800
16 N3 -15.0160 48.4830 -13.7840 n3 1 MOL -0.725600
17 C12 -16.2050 48.7020 -14.6700 c3 1 MOL 0.130800
18 C13 -16.6810 47.3690 -15.3030 c3 1 MOL 0.181800
19 C14 -14.4450 49.7610 -13.2480 c3 1 MOL 0.212100
20 C15 -13.1440 49.5400 -12.5600 ca 1 MOL -0.083300
21 C16 -12.7260 50.3710 -11.4950 ca 1 MOL -0.114500
22 C17 -11.5330 50.1010 -10.8010 ca 1 MOL -0.135000
23 C18 -10.7270 48.9940 -11.1520 ca 1 MOL -0.083300
24 C19 -11.1180 48.1990 -12.2540 ca 1 MOL -0.135000
25 C20 -12.3130 48.4650 -12.9450 ca 1 MOL -0.114500
26 C21 -9.5150 48.6440 -10.3570 c3 1 MOL -0.036100
27 C22 -9.5450 49.2100 -8.9070 c3 1 MOL -0.108400
28 C23 -9.5370 48.1130 -7.7970 c3 1 MOL 0.168800
29 N4 -8.2470 47.9380 -7.0490 n3 1 MOL -0.742600
30 C24 -6.9940 47.9100 -7.9010 c3 1 MOL 0.153800
31 C25 -6.7630 46.5630 -8.6780 c3 1 MOL 0.171800
32 N5 -6.7080 45.4300 -7.7290 n3 1 MOL -0.822700
33 C26 -7.0970 44.0430 -8.0770 c3 1 MOL 0.170800
34 H1 -5.8280 45.4380 -7.2070 hn 1 MOL 0.377300
35 C27 -7.4840 43.2580 -6.7780 c3 1 MOL 0.155300
36 N6 -8.5920 43.9270 -6.0360 n3 1 MOL -0.858200
37 C28 -8.6550 43.9260 -4.5460 c3 1 MOL 0.155300
38 H2 -9.4980 43.6710 -6.4350 hn 1 MOL 0.380800
39 C29 -9.2540 45.2630 -3.9900 c3 1 MOL 0.170800
40 N7 -8.4470 46.4140 -4.4580 n3 1 MOL -0.822700
41 C30 -8.9680 47.7960 -4.5640 c3 1 MOL 0.171800
42 H3 -7.5210 46.4090 -4.0220 hn 1 MOL 0.377300
43 C31 -8.1940 48.5850 -5.6810 c3 1 MOL 0.153800
44 C32 -21.2130 47.0070 -16.9020 cx 1 MOL 0.171500
45 C33 -20.4890 48.3320 -16.5700 cx 1 MOL -0.139400
46 C34 -22.0060 48.3230 -16.7370 cx 1 MOL -0.139400
47 C35 -24.3650 43.9460 -14.8680 c 1 MOL 0.930800
48 O2 -24.7570 42.9790 -14.0020 o 1 MOL -0.815300
49 O3 -25.2640 44.3630 -15.6320 o 1 MOL -0.815300
50 H4 -14.9350 45.6770 -13.9570 h1 1 MOL 0.062950
51 H5 -16.0650 45.4200 -12.6100 h1 1 MOL 0.062950
52 H6 -14.3700 47.2570 -12.1690 h1 1 MOL 0.037700
53 H7 -16.0460 47.8000 -12.0510 h1 1 MOL 0.037700
54 H8 -15.9440 49.4060 -15.4600 h1 1 MOL 0.037700
55 H9 -17.0170 49.1370 -14.0870 h1 1 MOL 0.037700
56 H10 -17.6240 47.5310 -15.8250 h1 1 MOL 0.062950
57 H11 -15.9340 47.0180 -16.0150 h1 1 MOL 0.062950
58 H12 -15.1520 50.2100 -12.5510 h1 1 MOL 0.038700
59 H13 -14.3070 50.4680 -14.0660 h1 1 MOL 0.038700
60 H14 -8.6270 49.0120 -10.8710 hc 1 MOL 0.046200
61 H15 -9.4070 47.5600 -10.3200 hc 1 MOL 0.046200
62 H16 -10.4240 49.8420 -8.7840 hc 1 MOL 0.045200
63 H17 -8.6950 49.8770 -8.7620 hc 1 MOL 0.045200
64 H18 -9.8320 47.1580 -8.2330 h1 1 MOL 0.053200
65 H19 -10.3400 48.3140 -7.0870 h1 1 MOL 0.053200
66 H20 -6.1270 48.1190 -7.2740 h1 1 MOL 0.031200
67 H21 -7.0220 48.7360 -8.6110 h1 1 MOL 0.031200
68 H22 -5.8250 46.6190 -9.2310 h1 1 MOL 0.039700
69 H23 -7.5790 46.4060 -9.3830 h1 1 MOL 0.039700
70 H24 -6.2610 43.5440 -8.5680 h1 1 MOL 0.040700
71 H25 -7.9500 44.0650 -8.7560 h1 1 MOL 0.040700
72 H26 -6.6110 43.1760 -6.1300 h1 1 MOL 0.027950
73 H27 -7.7850 42.2450 -7.0430 h1 1 MOL 0.027950
74 H28 -7.6540 43.7810 -4.1410 h1 1 MOL 0.027950
75 H29 -9.2650 43.0880 -4.2090 h1 1 MOL 0.027950
76 H30 -9.2510 45.2370 -2.9000 h1 1 MOL 0.040700
77 H31 -10.2810 45.3740 -4.3390 h1 1 MOL 0.040700
78 H32 -8.8440 48.3050 -3.6080 h1 1 MOL 0.039700
79 H33 -10.0290 47.7660 -4.8100 h1 1 MOL 0.039700
80 H34 -8.5880 49.5990 -5.7460 h1 1 MOL 0.031200
81 H35 -7.1540 48.7090 -5.3800 h1 1 MOL 0.031200
82 H36 -21.0990 46.6460 -17.9240 h1 1 MOL 0.078700
83 H37 -20.2040 48.6330 -17.5780 hc 1 MOL 0.076950
84 H38 -20.4320 48.2330 -15.4860 hc 1 MOL 0.076950
85 H39 -22.2970 48.2220 -15.6910 hc 1 MOL 0.076950
86 H40 -22.0690 48.6220 -17.7830 hc 1 MOL 0.076950
87 H41 -23.4740 45.8660 -16.4140 h4 1 MOL 0.170000
88 H42 -18.9470 47.0140 -15.7080 ha 1 MOL 0.132000
89 H43 -19.8900 43.1590 -12.5670 ha 1 MOL 0.170000
90 H44 -12.5930 47.8370 -13.7780 ha 1 MOL 0.140500
91 H45 -11.2230 50.7430 -9.9890 ha 1 MOL 0.128500
92 H46 -13.3250 51.2230 -11.2070 ha 1 MOL 0.140500
93 H47 -10.4960 47.3760 -12.5740 ha 1 MOL 0.128500
.<TRIPOS>BOND
1 1 2 ar
2 1 6 ar
3 1 12 1
4 2 3 ar
5 2 13 1
6 3 4 ar
7 3 88 1
8 4 5 ar
9 4 7 1
10 5 6 ar
11 5 10 1
12 6 89 1
13 7 8 1
14 7 44 1
15 8 9 2
16 8 87 1
17 9 10 1
18 9 47 1
19 10 11 2
20 13 14 1
21 13 18 1
22 14 15 1
23 14 50 1
24 14 51 1
25 15 16 1
26 15 52 1
27 15 53 1
28 16 17 1
29 16 19 1
30 17 18 1
31 17 54 1
32 17 55 1
33 18 56 1
34 18 57 1
35 19 20 1
36 19 58 1
37 19 59 1
38 20 21 ar
39 20 25 ar
40 21 22 ar
41 21 92 1
42 22 23 ar
43 22 91 1
44 23 24 ar
45 23 26 1
46 24 25 ar
47 24 93 1
48 25 90 1
49 26 27 1
50 26 60 1
51 26 61 1
52 27 28 1
53 27 62 1
54 27 63 1
55 28 29 1
56 28 64 1
57 28 65 1
58 29 30 1
59 29 43 1
60 30 31 1
61 30 66 1
62 30 67 1
63 31 32 1
64 31 68 1
65 31 69 1
66 32 33 1
67 32 34 1
68 33 35 1
69 33 70 1
70 33 71 1
71 35 36 1
72 35 72 1
73 35 73 1
74 36 37 1
75 36 38 1
76 37 39 1
77 37 74 1
78 37 75 1
79 39 40 1
80 39 76 1
81 39 77 1
82 40 41 1
83 40 42 1
84 41 43 1
85 41 78 1
86 41 79 1
87 43 80 1
88 43 81 1
89 44 45 1
90 44 46 1
91 44 82 1
92 45 46 1
93 45 83 1
94 45 84 1
95 46 85 1
96 46 86 1
97 47 48 1
98 47 49 1
.<TRIPOS>SUBSTRUCTURE
1 MOL 1 TEMP 0 **** **** 0 ROOT
Best,
Fabian
Fabian Glaser PhD
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Web
http://bku.technion.ac.il/
Tel +972 (0) 4 8293701
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Received on Thu Jun 20 2019 - 06:00:02 PDT
