AMBER Archive (2008)

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

From: Junmei Wang (junmwang_at_gmail.com)
Date: Tue Jan 22 2008 - 11:56:55 CST

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_at_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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