AMBER Archive (2008)

Subject: Re: AMBER: about AM1-BCC in antechamber

From: Shun Zhu (id4zs2008_at_gmail.com)
Date: Tue Jan 22 2008 - 11:38:01 CST

Hi Junmei:

         The following is my molecule: SB203580.pdb in PDB format
HETATM 1 CD1 SB2 1 7.550 16.360 31.280 1.00 20.00 C
HETATM 2 HD1 SB2 1 7.091 17.040 31.852 1.00 20.00 H
HETATM 3 CD2 SB2 1 8.830 15.890 31.620 1.00 20.00 C
HETATM 4 HD2 SB2 1 9.295 16.230 32.437 1.00 20.00 H
HETATM 5 CD3 SB2 1 9.450 14.930 30.790 1.00 20.00 C
HETATM 6 FD3 SB2 1 10.680 14.470 31.120 1.00 20.00 F
HETATM 7 CD4 SB2 1 8.830 14.430 29.630 1.00 20.00 C
HETATM 8 HD4 SB2 1 9.292 13.752 29.058 1.00 20.00 H
HETATM 9 CD5 SB2 1 7.550 14.900 29.290 1.00 20.00 C
HETATM 10 HD5 SB2 1 7.088 14.560 28.470 1.00 20.00 H
HETATM 11 CD6 SB2 1 6.920 15.860 30.120 1.00 20.00 C
HETATM 12 CC4 SB2 1 5.640 16.320 29.790 1.00 20.00 C
HETATM 13 NC3 SB2 1 5.300 17.510 29.270 1.00 20.00 N
HETATM 14 CC2 SB2 1 3.980 17.530 29.110 1.00 20.00 C
HETATM 15 CA6 SB2 1 3.210 18.570 28.590 1.00 20.00 C
HETATM 16 CA1 SB2 1 2.480 19.390 29.470 1.00 20.00 C
HETATM 17 HA1 SB2 1 2.536 19.249 30.458 1.00 20.00 H
HETATM 18 CA2 SB2 1 1.670 20.410 28.940 1.00 20.00 C
HETATM 19 HA2 SB2 1 1.149 21.009 29.548 1.00 20.00 H
HETATM 20 CA3 SB2 1 1.600 20.580 27.540 1.00 20.00 C
HETATM 21 S1 SB2 1 0.560 21.820 26.860 1.00 20.00 S
HETATM 22 C1 SB2 1 1.010 23.430 27.480 1.00 20.00 C
HETATM 23 H11 SB2 1 1.947 23.645 27.203 1.00 20.00 H
HETATM 24 H12 SB2 1 0.387 24.117 27.107 1.00 20.00 H
HETATM 25 H13 SB2 1 0.949 23.432 28.478 1.00 20.00 H
HETATM 26 O2 SB2 1 -0.780 21.540 27.270 1.00 20.00 O
HETATM 27 CA4 SB2 1 2.340 19.760 26.660 1.00 20.00 C
HETATM 28 HA4 SB2 1 2.289 19.903 25.672 1.00 20.00 H
HETATM 29 CA5 SB2 1 3.150 18.740 27.190 1.00 20.00 C
HETATM 30 HA5 SB2 1 3.676 18.144 26.584 1.00 20.00 H
HETATM 31 NC1 SB2 1 3.470 16.370 29.510 1.00 20.00 N
HETATM 32 HC1 SB2 1 2.500 16.120 29.500 1.00 20.00 H
HETATM 33 CC5 SB2 1 4.460 15.590 29.940 1.00 20.00 C
HETATM 34 CB4 SB2 1 4.350 14.300 30.450 1.00 20.00 C
HETATM 35 CB3 SB2 1 4.040 13.250 29.550 1.00 20.00 C
HETATM 36 HB3 SB2 1 3.904 13.426 28.575 1.00 20.00 H
HETATM 37 CB2 SB2 1 3.930 11.950 30.080 1.00 20.00 C
HETATM 38 HB2 SB2 1 3.713 11.177 29.484 1.00 20.00 H
HETATM 39 NB1 SB2 1 4.120 11.760 31.400 1.00 20.00 N
HETATM 40 CB6 SB2 1 4.410 12.730 32.290 1.00 20.00 C
HETATM 41 HB6 SB2 1 4.531 12.512 33.259 1.00 20.00 H
HETATM 42 CB5 SB2 1 4.540 14.060 31.830 1.00 20.00 C
HETATM 43 HB5 SB2 1 4.759 14.806 32.459 1.00 20.00 H

then I type in 'antechamber -i SB203580.pdb -fi pdb -o SB203580.mol2
-fo mol2 -c bcc'

the resulting ANTECHAMBER_AM1BCC_PRE.AC looks like the following:
CHARGE 0.00 ( 0 )
Formula: H16 C21 N3 O1 F1 S1
ATOM 1 CD1 SB2 1 7.550 16.360 31.280 -0.075300 ca
ATOM 2 HD1 SB2 1 7.091 17.040 31.852 0.154300 ha
ATOM 3 CD2 SB2 1 8.830 15.890 31.620 -0.172100 ca
ATOM 4 HD2 SB2 1 9.295 16.230 32.437 0.150600 ha
ATOM 5 CD3 SB2 1 9.450 14.930 30.790 0.094200 ca
ATOM 6 FD3 SB2 1 10.680 14.470 31.120 -0.105400 f
ATOM 7 CD4 SB2 1 8.830 14.430 29.630 -0.170800 ca
ATOM 8 HD4 SB2 1 9.292 13.752 29.058 0.150400 ha
ATOM 9 CD5 SB2 1 7.550 14.900 29.290 -0.095200 ca
ATOM 10 HD5 SB2 1 7.088 14.560 28.470 0.144200 ha
ATOM 11 CD6 SB2 1 6.920 15.860 30.120 -0.024200 ca
ATOM 12 CC4 SB2 1 5.640 16.320 29.790 -0.048700 cc
ATOM 13 NC3 SB2 1 5.300 17.510 29.270 -0.120300 nc
ATOM 14 CC2 SB2 1 3.980 17.530 29.110 -0.000400 cd
ATOM 15 CA6 SB2 1 3.210 18.570 28.590 0.018700 ca
ATOM 16 CA1 SB2 1 2.480 19.390 29.470 -0.142900 ca
ATOM 17 HA1 SB2 1 2.536 19.249 30.458 0.133200 ha
ATOM 18 CA2 SB2 1 1.670 20.410 28.940 -0.050500 ca
ATOM 19 HA2 SB2 1 1.149 21.009 29.548 0.169200 ha
ATOM 20 CA3 SB2 1 1.600 20.580 27.540 -0.550300 ca
ATOM 21 S1 SB2 1 0.560 21.820 26.860 1.453500 sx
ATOM 22 C1 SB2 1 1.010 23.430 27.480 -0.672600 c3
ATOM 23 H11 SB2 1 1.947 23.645 27.203 0.117100 h1
ATOM 24 H12 SB2 1 0.387 24.117 27.107 0.126200 h1
ATOM 25 H13 SB2 1 0.949 23.432 28.478 0.132700 h1
ATOM 26 O2 SB2 1 -0.780 21.540 27.270 -0.781700 o
ATOM 27 CA4 SB2 1 2.340 19.760 26.660 -0.068000 ca
ATOM 28 HA4 SB2 1 2.289 19.903 25.672 0.133500 ha
ATOM 29 CA5 SB2 1 3.150 18.740 27.190 -0.108000 ca
ATOM 30 HA5 SB2 1 3.676 18.144 26.584 0.161000 ha
ATOM 31 NC1 SB2 1 3.470 16.370 29.510 -0.182200 na
ATOM 32 HC1 SB2 1 2.500 16.120 29.500 0.259500 hn
ATOM 33 CC5 SB2 1 4.460 15.590 29.940 -0.064800 cd
ATOM 34 CB4 SB2 1 4.350 14.300 30.450 0.020300 ca
ATOM 35 CB3 SB2 1 4.040 13.250 29.550 -0.184400 ca
ATOM 36 HB3 SB2 1 3.904 13.426 28.575 0.141500 ha
ATOM 37 CB2 SB2 1 3.930 11.950 30.080 -0.068800 ca
ATOM 38 HB2 SB2 1 3.713 11.177 29.484 0.162300 h4
ATOM 39 NB1 SB2 1 4.120 11.760 31.400 -0.131200 nb
ATOM 40 CB6 SB2 1 4.410 12.730 32.290 -0.069100 ca
ATOM 41 HB6 SB2 1 4.531 12.512 33.259 0.165400 h4
ATOM 42 CB5 SB2 1 4.540 14.060 31.830 -0.161100 ca
ATOM 43 HB5 SB2 1 4.759 14.806 32.459 0.160200 ha
BOND 1 1 2 1 CD1 HD1
BOND 2 1 3 7 CD1 CD2
BOND 3 1 11 8 CD1 CD6
BOND 4 3 4 1 CD2 HD2
BOND 5 3 5 8 CD2 CD3
BOND 6 5 6 1 CD3 FD3
BOND 7 5 7 7 CD3 CD4
BOND 8 7 8 1 CD4 HD4
BOND 9 7 9 8 CD4 CD5
BOND 10 9 10 1 CD5 HD5
BOND 11 9 11 7 CD5 CD6
BOND 12 11 12 1 CD6 CC4
BOND 13 12 13 7 CC4 NC3
BOND 14 12 33 8 CC4 CC5
BOND 15 13 14 8 NC3 CC2
BOND 16 14 15 1 CC2 CA6
BOND 17 14 31 7 CC2 NC1
BOND 18 15 16 7 CA6 CA1
BOND 19 15 29 8 CA6 CA5
BOND 20 16 17 1 CA1 HA1
BOND 21 16 18 8 CA1 CA2
BOND 22 18 19 1 CA2 HA2
BOND 23 18 20 7 CA2 CA3
BOND 24 20 21 1 CA3 S1
BOND 25 20 27 8 CA3 CA4
BOND 26 21 22 1 S1 C1
BOND 27 21 26 2 S1 O2
BOND 28 22 23 1 C1 H11
BOND 29 22 24 1 C1 H12
BOND 30 22 25 1 C1 H13
BOND 31 27 28 1 CA4 HA4
BOND 32 27 29 7 CA4 CA5
BOND 33 29 30 1 CA5 HA5
BOND 34 31 32 1 NC1 HC1
BOND 35 31 33 7 NC1 CC5
BOND 36 33 34 1 CC5 CB4
BOND 37 34 35 7 CB4 CB3
BOND 38 34 42 8 CB4 CB5
BOND 39 35 36 1 CB3 HB3
BOND 40 35 37 8 CB3 CB2
BOND 41 37 38 1 CB2 HB2
BOND 42 37 39 7 CB2 NB1
BOND 43 39 40 8 NB1 CB6
BOND 44 40 41 1 CB6 HB6
BOND 45 40 42 7 CB6 CB5
BOND 46 42 43 1 CB5 HB5

the resulting ANTECHAMBER_AM1BCC.AC looks like the following:
CHARGE 0.00 ( 0 )
Formula: H16 C21 N3 O1 F1 S1
ATOM 1 CD1 SB2 1 7.550 16.360 31.280 -0.075300 16
ATOM 2 HD1 SB2 1 7.091 17.040 31.852 0.154300 91
ATOM 3 CD2 SB2 1 8.830 15.890 31.620 -0.172100 16
ATOM 4 HD2 SB2 1 9.295 16.230 32.437 0.150600 91
ATOM 5 CD3 SB2 1 9.450 14.930 30.790 0.129100 16
ATOM 6 FD3 SB2 1 10.680 14.470 31.120 -0.140300 71
ATOM 7 CD4 SB2 1 8.830 14.430 29.630 -0.170800 16
ATOM 8 HD4 SB2 1 9.292 13.752 29.058 0.150400 91
ATOM 9 CD5 SB2 1 7.550 14.900 29.290 -0.095200 16
ATOM 10 HD5 SB2 1 7.088 14.560 28.470 0.144200 91
ATOM 11 CD6 SB2 1 6.920 15.860 30.120 -0.131700 16
ATOM 12 CC4 SB2 1 5.640 16.320 29.790 0.387100 17
ATOM 13 NC3 SB2 1 5.300 17.510 29.270 -0.646300 24
ATOM 14 CC2 SB2 1 3.980 17.530 29.110 0.458600 17
ATOM 15 CA6 SB2 1 3.210 18.570 28.590 -0.088800 16
ATOM 16 CA1 SB2 1 2.480 19.390 29.470 -0.142900 16
ATOM 17 HA1 SB2 1 2.536 19.249 30.458 0.133200 91
ATOM 18 CA2 SB2 1 1.670 20.410 28.940 -0.050500 16
ATOM 19 HA2 SB2 1 1.149 21.009 29.548 0.169200 91
ATOM 20 CA3 SB2 1 1.600 20.580 27.540 -0.121800 16
ATOM 21 S1 SB2 1 0.560 21.820 26.860 0.326900 52
ATOM 22 C1 SB2 1 1.010 23.430 27.480 -0.128400 11
ATOM 23 H11 SB2 1 1.947 23.645 27.203 0.077800 91
ATOM 24 H12 SB2 1 0.387 24.117 27.107 0.086900 91
ATOM 25 H13 SB2 1 0.949 23.432 28.478 0.093400 91
ATOM 26 O2 SB2 1 -0.780 21.540 27.270 -0.509900 31
ATOM 27 CA4 SB2 1 2.340 19.760 26.660 -0.068000 16
ATOM 28 HA4 SB2 1 2.289 19.903 25.672 0.133500 91
ATOM 29 CA5 SB2 1 3.150 18.740 27.190 -0.108000 16
ATOM 30 HA5 SB2 1 3.676 18.144 26.584 0.161000 91
ATOM 31 NC1 SB2 1 3.470 16.370 29.510 -0.296100 23
ATOM 32 HC1 SB2 1 2.500 16.120 29.500 0.309200 91
ATOM 33 CC5 SB2 1 4.460 15.590 29.940 -0.154400 16
ATOM 34 CB4 SB2 1 4.350 14.300 30.450 0.020300 16
ATOM 35 CB3 SB2 1 4.040 13.250 29.550 -0.249700 16
ATOM 36 HB3 SB2 1 3.904 13.426 28.575 0.141500 91
ATOM 37 CB2 SB2 1 3.930 11.950 30.080 0.396400 17
ATOM 38 HB2 SB2 1 3.713 11.177 29.484 0.025400 91
ATOM 39 NB1 SB2 1 4.120 11.760 31.400 -0.657200 24
ATOM 40 CB6 SB2 1 4.410 12.730 32.290 0.396100 17
ATOM 41 HB6 SB2 1 4.531 12.512 33.259 0.028500 91
ATOM 42 CB5 SB2 1 4.540 14.060 31.830 -0.226400 16
ATOM 43 HB5 SB2 1 4.759 14.806 32.459 0.160200 91
BOND 1 1 2 1 CD1 HD1
BOND 2 1 3 7 CD1 CD2
BOND 3 1 11 8 CD1 CD6
BOND 4 3 4 1 CD2 HD2
BOND 5 3 5 8 CD2 CD3
BOND 6 5 6 1 CD3 FD3
BOND 7 5 7 7 CD3 CD4
BOND 8 7 8 1 CD4 HD4
BOND 9 7 9 8 CD4 CD5
BOND 10 9 10 1 CD5 HD5
BOND 11 9 11 7 CD5 CD6
BOND 12 11 12 1 CD6 CC4
BOND 13 12 13 7 CC4 NC3
BOND 14 12 33 8 CC4 CC5
BOND 15 13 14 8 NC3 CC2
BOND 16 14 15 1 CC2 CA6
BOND 17 14 31 7 CC2 NC1
BOND 18 15 16 7 CA6 CA1
BOND 19 15 29 8 CA6 CA5
BOND 20 16 17 1 CA1 HA1
BOND 21 16 18 8 CA1 CA2
BOND 22 18 19 1 CA2 HA2
BOND 23 18 20 7 CA2 CA3
BOND 24 20 21 1 CA3 S1
BOND 25 20 27 8 CA3 CA4
BOND 26 21 22 1 S1 C1
BOND 27 21 26 2 S1 O2
BOND 28 22 23 1 C1 H11
BOND 29 22 24 1 C1 H12
BOND 30 22 25 1 C1 H13
BOND 31 27 28 1 CA4 HA4
BOND 32 27 29 7 CA4 CA5
BOND 33 29 30 1 CA5 HA5
BOND 34 31 32 1 NC1 HC1
BOND 35 31 33 7 NC1 CC5
BOND 36 33 34 1 CC5 CB4
BOND 37 34 35 7 CB4 CB3
BOND 38 34 42 8 CB4 CB5
BOND 39 35 36 1 CB3 HB3
BOND 40 35 37 8 CB3 CB2
BOND 41 37 38 1 CB2 HB2
BOND 42 37 39 7 CB2 NB1
BOND 43 39 40 8 NB1 CB6
BOND 44 40 41 1 CB6 HB6
BOND 45 40 42 7 CB6 CB5
BOND 46 42 43 1 CB5 HB5

If you compare the charges, you will find atoms 1,2,3,4, 7,8,9,10,
16,17,18,19, 27,28,29,30, 34,36,43 have the same charges in the two
files. I read C. Bayly's paper about AM1BCC parameterization and
found they assigned zeros to some bonds' BCC values. Maybe those atoms
(1,2,3,4.....) are supposed to have zero correction? I appreciate it a
lot if you can help me with this. Thanks

Shun
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