Hi friends
I am trying to create topology files for drug molecules to be used for
gromacs simulation with amberff , I have a fermi gpu and my simulation is a
terinary protein complex and right now I can only use amberff to be working
with GPU. out of 2 ligands one which is farnysl pyro phosphate (FPP) which
antechamber successfully generated topology files and with the other one
which is tipifarnib (drug molecule) I am getting stuck at sqm: out, I double
checked the structure and connectivity and everything seems fine ( I am
doing this with Marvin and babel and I don't have sybyl) the out put error
is:
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.1518E+07 DeltaE = -0.2626E+01 DeltaP = 0.3996E-01
QMMM: Smallest DeltaE = -0.2490E-10 DeltaP = 0.5095E-06 Step = 914
I have energy minimized and corrected the bonds.
The same error also comes when I try with a different ligand theaflavin
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.2034E+07 DeltaE = 0.1099E-09 DeltaP = 0.5351E-13
QMMM: Smallest DeltaE = 0.1099E-09 DeltaP = 0.2959E-07 Step = 2
Is there a way to bypass this and make it pass.
### the mol files are tipifarnib ##
.<TRIPOS>MOLECULE
jan-yas2.pdb
86 90 0 0 0
SMALL
GASTEIGER
Energy = 0
.<TRIPOS>ATOM
1 CL1 18.2050 131.3320 -4.6480 Cl 0 UNK0 -0.1218
2 CL2 13.7830 132.8000 -3.0670 Cl 0 UNK0 -0.1218
3 C1 21.8010 132.4450 1.5010 C.3 0 UNK0 -0.1055
4 1H1 22.2130 131.5190 1.9310 H 0 UNK0 0.0023
5 2H1 22.2860 133.3050 1.9860 H 0 UNK0 0.0023
6 3H1 22.0420 132.4410 0.4290 H 0 UNK0 0.0023
7 N1 20.3350 132.4680 1.7050 N.4 0 UNK0 0.3676
8 HN1 19.9530 131.8230 1.0380 H 0 UNK0 -0.0848
9 O1 13.1490 138.8730 1.6960 O.3 0 UNK0 -0.4097
10 HO1 12.4880 139.3750 1.2330 H 0 UNK0 0.2071
11 C2 20.0160 131.9210 3.0400 C.3 0 UNK0 -0.1373
12 1H2 20.0000 130.8200 3.0170 H 0 UNK0 -0.0147
13 2H2 20.7720 132.2490 3.7710 H 0 UNK0 -0.0147
14 N2 18.6980 132.4500 3.4390 N.4 0 UNK0 0.3684
15 1HN2 18.0130 131.7090 3.4730 H 0 UNK0 -0.0888
16 2HN2 18.7440 132.8700 4.3560 H 0 UNK0 -0.0888
17 C3 18.3270 133.4620 2.4340 C.3 0 UNK0 -0.1097
18 1H3 17.9170 134.3600 2.9150 H 0 UNK0 0.0037
19 2H3 17.5710 133.0200 1.7760 H 0 UNK0 0.0037
20 N3 20.8880 135.1770 0.1560 N.4 0 UNK0 0.3811
21 1HN3 20.9510 135.9440 -0.4920 H 0 UNK0 -0.0893
22 2HN3 21.5590 134.5150 -0.1890 H 0 UNK0 -0.0893
23 3HN3 21.2900 135.5680 0.9930 H 0 UNK0 -0.0893
24 C4 19.6470 133.7790 1.7030 C.3 0 UNK0 -0.1067
25 H4 20.2100 134.3550 2.4480 H 0 UNK0 0.0061
26 N4 15.4270 138.4370 2.0460 N.4 0 UNK0 0.3971
27 HN4 15.0090 137.5780 2.3710 H 0 UNK0 -0.0780
28 C5 19.5270 134.6080 0.3660 C.3 0 UNK0 -0.0795
29 C6 19.2190 133.6980 -0.8860 C.3 0 UNK0 -0.0524
30 H6 20.0850 133.0300 -0.9920 H 0 UNK0 0.0287
31 C7 17.9860 132.7430 -0.8060 C.3 0 UNK0 -0.0502
32 1H7 18.2460 131.8350 -0.2490 H 0 UNK0 0.0268
33 2H7 17.0990 133.1780 -0.3380 H 0 UNK0 0.0268
34 C8 17.5160 132.2610 -2.1960 C.3 0 UNK0 -0.0365
35 1H8 16.9850 131.3030 -2.0870 H 0 UNK0 0.0279
36 2H8 16.8290 132.9950 -2.6320 H 0 UNK0 0.0279
37 C9 18.7170 132.1010 -3.1400 C.3 0 UNK0 0.0340
38 H9 19.4690 131.4600 -2.6580 H 0 UNK0 0.0465
39 C10 19.3010 133.4980 -3.4420 C.3 0 UNK0 -0.0365
40 1H10 18.7600 133.9480 -4.2890 H 0 UNK0 0.0279
41 2H10 20.3570 133.3750 -3.7230 H 0 UNK0 0.0279
42 C11 19.1720 134.4620 -2.2370 C.3 0 UNK0 -0.0502
43 1H11 19.9900 135.1880 -2.3350 H 0 UNK0 0.0268
44 2H11 18.2220 135.0030 -2.3390 H 0 UNK0 0.0268
45 C12 18.6130 135.8930 0.4590 C.3 0 UNK0 -0.0523
46 H12 18.8580 136.4570 -0.4510 H 0 UNK0 0.0287
47 C13 17.0740 135.7760 0.3110 C.3 0 UNK0 -0.0499
48 1H13 16.8800 135.2600 -0.6270 H 0 UNK0 0.0270
49 2H13 16.5860 135.2380 1.1350 H 0 UNK0 0.0270
50 C14 16.4650 137.1890 0.1140 C.3 0 UNK0 -0.0497
51 H14 17.0320 137.6740 -0.6950 H 0 UNK0 0.0288
52 C15 18.9540 136.8750 1.6150 C.3 0 UNK0 -0.0529
53 1H15 19.5440 136.4020 2.4080 H 0 UNK0 0.0267
54 2H15 19.5400 137.7140 1.2110 H 0 UNK0 0.0267
55 C16 17.7030 137.4450 2.3230 C.3 0 UNK0 -0.0647
56 1H16 17.2040 136.6430 2.8860 H 0 UNK0 0.0250
57 2H16 18.0640 138.1970 3.0390 H 0 UNK0 0.0250
58 C17 16.6900 138.0990 1.3520 C.3 0 UNK0 -0.0718
59 H17 17.1350 139.0420 0.9970 H 0 UNK0 0.0098
60 C18 15.6230 139.2840 3.2440 C.3 0 UNK0 -0.0994
61 1H18 14.6510 139.6520 3.6060 H 0 UNK0 0.0025
62 2H18 16.2580 140.1500 3.0020 H 0 UNK0 0.0025
63 3H18 16.0870 138.7140 4.0620 H 0 UNK0 0.0025
64 C19 14.4580 139.1210 1.1630 C.3 0 UNK0 0.0241
65 H19 14.6290 140.2100 1.1780 H 0 UNK0 0.0385
66 C20 14.5300 138.6520 -0.3070 C.3 0 UNK0 -0.0390
67 1H20 13.5320 138.8000 -0.7420 H 0 UNK0 0.0273
68 2H20 15.2530 139.2780 -0.8520 H 0 UNK0 0.0273
69 C21 14.9880 137.1770 -0.3780 C.3 0 UNK0 -0.0362
70 H21 14.3540 136.5970 0.3090 H 0 UNK0 0.0306
71 C22 14.8710 136.5600 -1.8130 C.3 0 UNK0 -0.0367
72 H22 15.8670 136.5400 -2.2790 H 0 UNK0 0.0304
73 C23 14.3150 135.1140 -1.7540 C.3 0 UNK0 -0.0336
74 1H23 14.8930 134.4780 -1.0700 H 0 UNK0 0.0282
75 2H23 13.2740 135.1340 -1.4020 H 0 UNK0 0.0282
76 C24 14.3570 134.4690 -3.1570 C.3 0 UNK0 0.0343
77 H24 15.3870 134.4760 -3.5420 H 0 UNK0 0.0465
78 C25 13.4770 135.2690 -4.1340 C.3 0 UNK0 -0.0367
79 1H25 13.5370 134.8140 -5.1350 H 0 UNK0 0.0279
80 2H25 12.4320 135.2550 -3.7920 H 0 UNK0 0.0279
81 C26 13.9940 136.7190 -4.1970 C.3 0 UNK0 -0.0515
82 1H26 15.0230 136.7260 -4.5890 H 0 UNK0 0.0266
83 2H26 13.3510 137.3000 -4.8740 H 0 UNK0 0.0266
84 C27 13.9700 137.3560 -2.7910 C.3 0 UNK0 -0.0499
85 1H27 12.9300 137.3690 -2.4320 H 0 UNK0 0.0268
86 2H27 14.3390 138.3850 -2.9050 H 0 UNK0 0.0268
.<TRIPOS>BOND
1 1 37 1
2 2 76 1
3 3 4 1
4 3 5 1
5 3 6 1
6 3 7 1
7 7 8 1
8 7 11 1
9 7 24 1
10 9 10 1
11 9 64 1
12 11 12 1
13 11 13 1
14 11 14 1
15 14 15 1
16 14 16 1
17 14 17 1
18 17 18 1
19 17 19 1
20 17 24 1
21 20 21 1
22 20 22 1
23 20 23 1
24 20 28 1
25 24 25 1
26 24 28 1
27 26 27 1
28 26 58 1
29 26 60 1
30 26 64 1
31 28 29 1
32 28 45 1
33 29 30 1
34 29 31 1
35 29 42 1
36 31 32 1
37 31 33 1
38 31 34 1
39 34 35 1
40 34 36 1
41 34 37 1
42 37 38 1
43 37 39 1
44 39 40 1
45 39 41 1
46 39 42 1
47 42 43 1
48 42 44 1
49 45 46 1
50 45 47 1
51 45 52 1
52 47 48 1
53 47 49 1
54 47 50 1
55 50 51 1
56 50 58 1
57 50 69 1
58 52 53 1
59 52 54 1
60 52 55 1
61 55 56 1
62 55 57 1
63 55 58 1
64 58 59 1
65 60 61 1
66 60 62 1
67 60 63 1
68 64 65 1
69 64 66 1
70 66 67 1
71 66 68 1
72 66 69 1
73 69 70 1
74 69 71 1
75 71 72 1
76 71 73 1
77 71 84 1
78 73 74 1
79 73 75 1
80 73 76 1
81 76 77 1
82 76 78 1
83 78 79 1
84 78 80 1
85 78 81 1
86 81 82 1
87 81 83 1
88 81 84 1
89 84 85 1
90 84 86 1
# the mol file of theaflavin ##
.<TRIPOS>MOLECULE
acd0119y.pdb
89 94 0 0 0
SMALL
GASTEIGER
Energy = 0
.<TRIPOS>ATOM
1 C 2.1830 2.8580 0.4350 C.3 0 UNK0 -0.0169
2 1H 2.4780 3.8060 0.3160 H 0 UNK0 0.0295
3 2H 2.3010 2.5890 1.3910 H 0 UNK0 0.0295
4 C 0.6700 2.7650 0.0810 C.3 0 UNK0 0.0820
5 H 0.1270 3.2710 0.7520 H 0 UNK0 0.0619
6 C 0.1890 1.2740 -0.0150 C.3 0 UNK0 0.0878
7 H -0.6840 1.2620 -0.5030 H 0 UNK0 0.0625
8 O 1.1150 0.5010 -0.8500 O.3 0 UNK0 -0.3701
9 C 2.5010 0.4900 -0.4120 C.3 0 UNK0 0.0667
10 H 2.4530 0.1400 0.5240 H 0 UNK0 0.0600
11 C 3.3670 -0.4920 -1.2500 C.3 0 UNK0 -0.0000
12 1H 3.0000 -1.4170 -1.1520 H 0 UNK0 0.0315
13 2H 3.3330 -0.2190 -2.2120 H 0 UNK0 0.0315
14 C 4.8480 -0.4740 -0.7640 C.3 0 UNK0 0.0600
15 H 4.9040 -0.8840 0.1460 H 0 UNK0 0.0595
16 C 5.4520 0.9620 -0.7580 C.3 0 UNK0 -0.0003
17 1H 6.3560 0.9260 -0.3320 H 0 UNK0 0.0315
18 2H 5.5410 1.2740 -1.7040 H 0 UNK0 0.0315
19 C 4.5770 1.9870 0.0230 C.3 0 UNK0 0.0628
20 H 4.6140 1.8300 1.0100 H 0 UNK0 0.0598
21 C 3.0880 1.9500 -0.4450 C.3 0 UNK0 0.0139
22 H 3.0900 2.2990 -1.3820 H 0 UNK0 0.0352
23 O 5.1360 3.2800 -0.1780 O.3 0 UNK0 -0.3913
24 HO 6.0900 3.2120 -0.2230 H 0 UNK0 0.2098
25 O 5.6430 -1.2950 -1.6080 O.3 0 UNK0 -0.3916
26 HO 5.8220 -2.1260 -1.1690 H 0 UNK0 0.2098
27 C -0.0970 0.5710 1.3510 C.3 0 UNK0 -0.0096
28 H 0.7910 0.5470 1.8100 H 0 UNK0 0.0327
29 C -1.0990 1.3100 2.2710 C.3 0 UNK0 -0.0191
30 1H -0.9850 2.2920 2.1210 H 0 UNK0 0.0294
31 2H -2.0220 1.0360 2.0000 H 0 UNK0 0.0294
32 C -0.9450 1.0370 3.7920 C.3 0 UNK0 0.0817
33 H -1.8480 1.2020 4.1880 H 0 UNK0 0.0619
34 O 0.0100 1.9660 4.2890 O.3 0 UNK0 -0.3892
35 HO 0.8540 1.5280 4.4010 H 0 UNK0 0.2099
36 C -0.5390 -0.3860 4.2870 C.3 0 UNK0 0.0865
37 H 0.4420 -0.5510 4.1830 H 0 UNK0 0.0623
38 C -1.1570 -1.6130 3.5150 C.3 0 UNK0 0.0190
39 H -2.0920 -1.4000 3.2330 H 0 UNK0 0.0355
40 C -0.3170 -1.8970 2.1930 C.3 0 UNK0 -0.0277
41 H 0.6430 -1.8270 2.4630 H 0 UNK0 0.0309
42 C -0.6930 -0.8350 1.1190 C.3 0 UNK0 -0.0441
43 1H -1.6890 -0.7470 1.1020 H 0 UNK0 0.0272
44 2H -0.3710 -1.1620 0.2300 H 0 UNK0 0.0272
45 C -0.4650 -3.3430 1.5610 C.3 0 UNK0 -0.0066
46 H -1.3580 -3.3520 1.1110 H 0 UNK0 0.0330
47 C -0.4250 -4.4320 2.6770 C.3 0 UNK0 -0.0189
48 1H -0.5690 -5.3300 2.2610 H 0 UNK0 0.0294
49 2H 0.4710 -4.4100 3.1210 H 0 UNK0 0.0294
50 C -1.5060 -4.2150 3.7520 C.3 0 UNK0 0.0818
51 H -2.4270 -4.2710 3.3670 H 0 UNK0 0.0619
52 C -1.2960 -2.8560 4.4630 C.3 0 UNK0 0.0865
53 H -0.4660 -2.9130 5.0180 H 0 UNK0 0.0623
54 O -2.4080 -2.6590 5.3310 O.3 0 UNK0 -0.3889
55 HO -3.2130 -2.6150 4.8140 H 0 UNK0 0.2099
56 O -1.4070 -5.2720 4.6970 O.3 0 UNK0 -0.3892
57 HO -1.3850 -4.9080 5.5820 H 0 UNK0 0.2099
58 C 0.6010 -3.6870 0.4450 C.3 0 UNK0 0.0880
59 H 1.4730 -3.5440 0.9130 H 0 UNK0 0.0625
60 C 0.5780 -5.1560 -0.1220 C.3 0 UNK0 0.0820
61 H 0.3840 -5.8090 0.6110 H 0 UNK0 0.0619
62 C -0.4590 -5.3370 -1.2670 C.3 0 UNK0 -0.0169
63 1H -0.3020 -6.2250 -1.6980 H 0 UNK0 0.0295
64 2H -1.3760 -5.3160 -0.8690 H 0 UNK0 0.0295
65 C -0.3740 -4.2380 -2.3620 C.3 0 UNK0 0.0139
66 H 0.4890 -4.3110 -2.8620 H 0 UNK0 0.0352
67 C -1.4770 -4.4200 -3.4530 C.3 0 UNK0 0.0628
68 H -2.3500 -4.6090 -3.0030 H 0 UNK0 0.0598
69 C -1.5870 -3.1890 -4.4040 C.3 0 UNK0 -0.0003
70 1H -0.7870 -3.1780 -5.0040 H 0 UNK0 0.0315
71 2H -2.4160 -3.2860 -4.9550 H 0 UNK0 0.0315
72 C -1.6540 -1.8310 -3.6450 C.3 0 UNK0 0.0600
73 H -2.5280 -1.7400 -3.1670 H 0 UNK0 0.0595
74 C -0.4740 -1.6730 -2.6430 C.3 0 UNK0 -0.0000
75 1H 0.3880 -1.6630 -3.1490 H 0 UNK0 0.0315
76 2H -0.5790 -0.8130 -2.1440 H 0 UNK0 0.0315
77 C -0.4560 -2.8500 -1.6300 C.3 0 UNK0 0.0667
78 H -1.2800 -2.7810 -1.0680 H 0 UNK0 0.0600
79 O 0.6320 -2.7350 -0.6710 O.3 0 UNK0 -0.3701
80 O -1.6310 -0.7640 -4.5830 O.3 0 UNK0 -0.3916
81 HO -1.6260 -1.1200 -5.4720 H 0 UNK0 0.2098
82 O -1.1750 -5.5530 -4.2600 O.3 0 UNK0 -0.3913
83 HO -1.1070 -6.3310 -3.7060 H 0 UNK0 0.2098
84 O 1.8710 -5.5060 -0.5970 O.3 0 UNK0 -0.3892
85 HO 2.4730 -5.5850 0.1430 H 0 UNK0 0.2099
86 O -0.8060 -0.3650 5.6910 O.3 0 UNK0 -0.3889
87 HO -1.7520 -0.3600 5.8360 H 0 UNK0 0.2099
88 O 0.4330 3.4220 -1.1600 O.3 0 UNK0 -0.3892
89 HO 0.3800 2.7720 -1.8610 H 0 UNK0 0.2099
.<TRIPOS>BOND
1 1 2 1
2 1 3 1
3 1 4 1
4 1 21 1
5 4 5 1
6 4 6 1
7 4 88 1
8 6 7 1
9 6 8 1
10 6 27 1
11 8 9 1
12 9 10 1
13 9 11 1
14 9 21 1
15 11 12 1
16 11 13 1
17 11 14 1
18 14 15 1
19 14 16 1
20 14 25 1
21 16 17 1
22 16 18 1
23 16 19 1
24 19 20 1
25 19 21 1
26 19 23 1
27 21 22 1
28 23 24 1
29 25 26 1
30 27 28 1
31 27 29 1
32 27 42 1
33 29 30 1
34 29 31 1
35 29 32 1
36 32 33 1
37 32 34 1
38 32 36 1
39 34 35 1
40 36 37 1
41 36 38 1
42 36 86 1
43 38 39 1
44 38 40 1
45 38 52 1
46 40 41 1
47 40 42 1
48 40 45 1
49 42 43 1
50 42 44 1
51 45 46 1
52 45 47 1
53 45 58 1
54 47 48 1
55 47 49 1
56 47 50 1
57 50 51 1
58 50 52 1
59 50 56 1
60 52 53 1
61 52 54 1
62 54 55 1
63 56 57 1
64 58 59 1
65 58 60 1
66 58 79 1
67 60 61 1
68 60 62 1
69 60 84 1
70 62 63 1
71 62 64 1
72 62 65 1
73 65 66 1
74 65 67 1
75 65 77 1
76 67 68 1
77 67 69 1
78 67 82 1
79 69 70 1
80 69 71 1
81 69 72 1
82 72 73 1
83 72 74 1
84 72 80 1
85 74 75 1
86 74 76 1
87 74 77 1
88 77 78 1
89 77 79 1
90 80 81 1
91 82 83 1
92 84 85 1
93 86 87 1
94 88 89 1
Any help is highly appreciated
regards
kala bharath
P.S : this is my first time using amber
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Received on Fri Feb 25 2011 - 08:00:03 PST
