Hi, Shun,
You have already got the answer. Yes, if the bcc parameter is 0, there is no
correction at all for the involved atoms.
Best
Junmei
On Jan 22, 2008 11:38 AM, Shun Zhu <id4zs2008.gmail.com> wrote:
> 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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Received on Wed Jan 23 2008 - 06:07:29 PST
