The input file is a pdb file:
REMARK 888
REMARK 888 WRITTEN BY MAESTRO (A PRODUCT OF SCHRODINGER, LLC)
TITLE Displayed atoms
MODEL 1
HETATM 1 N1 PP1 A 532 26.370 31.633 39.586 1.00 16.92 N
HETATM 2 C2 PP1 A 532 26.550 29.232 36.919 1.00 15.69 C
HETATM 3 N3 PP1 A 532 26.957 30.344 37.535 1.00 14.95 N
HETATM 4 C4 PP1 A 532 26.252 30.577 38.681 1.00 19.51 C
HETATM 5 C5 PP1 A 532 25.208 29.760 39.194 1.00 18.34 C
HETATM 6 C6 PP1 A 532 24.886 28.624 38.410 1.00 18.09 C
HETATM 7 N7 PP1 A 532 25.581 28.385 37.278 1.00 16.77 N
HETATM 8 N8 PP1 A 532 25.484 31.512 40.619 1.00 19.06 N
HETATM 9 C9 PP1 A 532 24.803 30.412 40.404 1.00 16.67 C
HETATM 10 N10 PP1 A 532 23.870 27.727 38.729 1.00 15.37 N
HETATM 11 C11 PP1 A 532 23.773 29.975 41.348 1.00 16.81 C
HETATM 12 C12 PP1 A 532 22.797 30.885 41.809 1.00 17.35 C
HETATM 13 C13 PP1 A 532 21.804 30.467 42.716 1.00 19.29 C
HETATM 14 C14 PP1 A 532 21.778 29.134 43.173 1.00 18.96 C
HETATM 15 C15 PP1 A 532 22.755 28.224 42.722 1.00 17.02 C
HETATM 16 C16 PP1 A 532 23.748 28.643 41.816 1.00 15.16 C
HETATM 17 C24 PP1 A 532 20.712 28.686 44.151 1.00 16.99 C
HETATM 18 C28 PP1 A 532 27.291 32.786 39.545 1.00 22.83 C
HETATM 19 C29 PP1 A 532 27.091 33.745 40.746 1.00 25.14 C
HETATM 20 C33 PP1 A 532 27.048 33.595 38.255 1.00 24.71 C
HETATM 21 C37 PP1 A 532 28.748 32.280 39.583 1.00 27.58 C
HETATM 22 H2 PP1 A 532 27.070 28.988 36.004 1.00 0.00 H
HETATM 23 H101 PP1 A 532 23.647 26.957 38.115 1.00 0.00 H
HETATM 24 H102 PP1 A 532 23.270 27.870 39.528 1.00 0.00 H
HETATM 25 H12 PP1 A 532 22.806 31.909 41.464 1.00 0.00 H
HETATM 26 H13 PP1 A 532 21.063 31.174 43.059 1.00 0.00 H
HETATM 27 H15 PP1 A 532 22.748 27.202 43.072 1.00 0.00 H
HETATM 28 H16 PP1 A 532 24.497 27.938 41.486 1.00 0.00 H
HETATM 29 H241 PP1 A 532 21.041 28.866 45.174 1.00 0.00 H
HETATM 30 H242 PP1 A 532 19.782 29.233 43.988 1.00 0.00 H
HETATM 31 H243 PP1 A 532 20.502 27.622 44.039 1.00 0.00 H
HETATM 32 H291 PP1 A 532 27.780 34.589 40.697 1.00 0.00 H
HETATM 33 H292 PP1 A 532 26.082 34.157 40.770 1.00 0.00 H
HETATM 34 H293 PP1 A 532 27.271 33.243 41.698 1.00 0.00 H
HETATM 35 H331 PP1 A 532 27.685 34.480 38.217 1.00 0.00 H
HETATM 36 H332 PP1 A 532 27.260 33.014 37.358 1.00 0.00 H
HETATM 37 H333 PP1 A 532 26.013 33.934 38.191 1.00 0.00 H
HETATM 38 H371 PP1 A 532 29.454 33.111 39.593 1.00 0.00 H
HETATM 39 H372 PP1 A 532 28.933 31.681 40.475 1.00 0.00 H
HETATM 40 H373 PP1 A 532 28.992 31.666 38.717 1.00 0.00 H
CONECT 1 4 8 18
CONECT 2 3 7 22
CONECT 2 3
CONECT 3 2 4
CONECT 3 2
CONECT 4 1 3 5
CONECT 4 5
CONECT 5 4 6 9
CONECT 5 4
CONECT 6 5 7 10
CONECT 6 7
CONECT 7 2 6
CONECT 7 6
CONECT 8 1 9
CONECT 8 9
CONECT 9 5 8 11
CONECT 9 8
CONECT 10 6 23 24
CONECT 11 9 12 16
CONECT 11 16
CONECT 12 11 13 25
CONECT 12 13
CONECT 13 12 14 26
CONECT 13 12
CONECT 14 13 15 17
CONECT 14 15
CONECT 15 14 16 27
CONECT 15 14
CONECT 16 11 15 28
CONECT 16 11
CONECT 17 14 29 30 31
CONECT 18 1 19 20 21
CONECT 19 18 32 33 34
CONECT 20 18 35 36 37
CONECT 21 18 38 39 40
CONECT 22 2
CONECT 23 10
CONECT 24 10
CONECT 25 12
CONECT 26 13
CONECT 27 15
CONECT 28 16
CONECT 29 17
CONECT 30 17
CONECT 31 17
CONECT 32 19
CONECT 33 19
CONECT 34 19
CONECT 35 20
CONECT 36 20
CONECT 37 20
CONECT 38 21
CONECT 39 21
CONECT 40 21
ENDMDL
END
The output is a mol2:
.<TRIPOS>MOLECULE
PP1
40 48 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 N1 26.3700 31.6330 39.5860 n3 532 PP1 -0.447400
2 C2 26.5500 29.2320 36.9190 c2 532 PP1 0.598100
3 N3 26.9570 30.3440 37.5350 n2 532 PP1 -0.629900
4 C4 26.2520 30.5770 38.6810 c3 532 PP1 0.366400
5 C5 25.2080 29.7600 39.1940 c3 532 PP1 -0.281000
6 C6 24.8860 28.6240 38.4100 c3 532 PP1 0.710600
7 N7 25.5810 28.3850 37.2780 nh 532 PP1 -0.743600
8 N8 25.4840 31.5120 40.6190 n3 532 PP1 -0.350400
9 C9 24.8030 30.4120 40.4040 c3 532 PP1 0.277400
10 N10 23.8700 27.7270 38.7290 n3 532 PP1 -0.921800
11 C11 23.7730 29.9750 41.3480 c3 532 PP1 -0.026000
12 C12 22.7970 30.8850 41.8090 c3 532 PP1 -0.058700
13 C13 21.8040 30.4670 42.7160 c3 532 PP1 -0.096700
14 C14 21.7780 29.1340 43.1730 c3 532 PP1 -0.061000
15 C15 22.7550 28.2240 42.7220 c3 532 PP1 -0.098700
16 C16 23.7480 28.6430 41.8160 c3 532 PP1 -0.080700
17 C24 20.7120 28.6860 44.1510 c3 532 PP1 -0.064100
18 C28 27.2910 32.7860 39.5450 c3 532 PP1 0.277200
19 C29 27.0910 33.7450 40.7460 c3 532 PP1 -0.105433
20 C33 27.0480 33.5950 38.2550 c3 532 PP1 -0.105433
21 C37 28.7480 32.2800 39.5830 c3 532 PP1 -0.105433
22 H2 27.0700 28.9880 36.0040 h5 532 PP1 0.057800
23 H101 23.6470 26.9570 38.1150 hn 532 PP1 0.439800
24 H102 23.2700 27.8700 39.5280 hn 532 PP1 0.439800
25 H12 22.8060 31.9090 41.4640 hc 532 PP1 0.105700
26 H13 21.0630 31.1740 43.0590 hc 532 PP1 0.095700
27 H15 22.7480 27.2020 43.0720 hc 532 PP1 0.095700
28 H16 24.4970 27.9380 41.4860 hc 532 PP1 0.105700
29 H241 21.0410 28.8660 45.1740 hc 532 PP1 0.046367
30 H242 19.7820 29.2330 43.9880 hc 532 PP1 0.046367
31 H243 20.5020 27.6220 44.0390 hc 532 PP1 0.046367
32 H291 27.7800 34.5890 40.6970 hc 532 PP1 0.052033
33 H292 26.0820 34.1570 40.7700 hc 532 PP1 0.052033
34 H293 27.2710 33.2430 41.6980 hc 532 PP1 0.052033
35 H331 27.6850 34.4800 38.2170 hc 532 PP1 0.052033
36 H332 27.2600 33.0140 37.3580 hc 532 PP1 0.052033
37 H333 26.0130 33.9340 38.1910 hc 532 PP1 0.052033
38 H371 29.4540 33.1110 39.5930 hc 532 PP1 0.052033
39 H372 28.9330 31.6810 40.4750 hc 532 PP1 0.052033
40 H373 28.9920 31.6660 38.7170 hc 532 PP1 0.052033
.<TRIPOS>BOND
1 1 4 1
2 1 8 1
3 1 18 1
4 2 3 2
5 2 7 1
6 2 22 1
7 3 4 1
8 4 5 1
9 4 5 1
10 5 6 1
11 5 9 1
12 6 7 1
13 6 7 1
14 6 10 1
15 8 9 1
16 8 9 1
17 9 11 1
18 10 23 1
19 10 24 1
20 11 12 1
21 11 16 1
22 11 16 1
23 12 13 1
24 12 13 1
25 12 25 1
26 13 14 1
27 13 26 1
28 14 15 1
29 14 15 1
30 14 17 1
31 15 16 1
32 15 27 1
33 16 28 1
34 17 29 1
35 17 30 1
36 17 31 1
37 18 19 1
38 18 20 1
39 18 21 1
40 19 32 1
41 19 33 1
42 19 34 1
43 20 35 1
44 20 36 1
45 20 37 1
46 21 38 1
47 21 39 1
48 21 40 1
.<TRIPOS>SUBSTRUCTURE
1 PP1 1 TEMP 0 **** **** 0 ROOT
I used the following command:
antechamber -i PP1.pdb -fi pdb -o PP1.mol2 -fo mol2 -c bcc -s 2
Any suggestion?
_______________________________
Valentina Romano | PhD Student |
Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics |
Klingelbergstrasse 61 | CH-4056 Basel |
Phone: +41 61 267 15 80
________________________________________
From: hannes.loeffler.stfc.ac.uk [hannes.loeffler.stfc.ac.uk]
Sent: Friday, February 20, 2015 12:05 PM
To: amber.ambermd.org
Subject: Re: [AMBER] ANTECHAMBER: error in mol2 file
Crucial information missing: what was the original input and how (detailled steps) did you get this mol2? The mol2 you have pasted here is incomplete and it shouldn't have 48 bonds.
________________________________________
From: Valentina Romano [valentina.romano.unibas.ch]
Sent: 20 February 2015 09:59
To: AMBER Mailing List
Subject: [AMBER] ANTECHAMBER: error in mol2 file
Dear Amber users
I am using antechamber to parametrize an inhibitor (PP1).
The inhibitor contains a condensate aromatic ring plus a benzene ring.
The mol2 file I obtained is the following:
.<TRIPOS>ATOM
1 N1 26.3700 31.6330 39.5860 n3 532 PP1 -0.447400
2 C2 26.5500 29.2320 36.9190 c2 532 PP1 0.598100
3 N3 26.9570 30.3440 37.5350 n2 532 PP1 -0.629900
4 C4 26.2520 30.5770 38.6810 c3 532 PP1 0.366400
5 C5 25.2080 29.7600 39.1940 c3 532 PP1 -0.281000
6 C6 24.8860 28.6240 38.4100 c3 532 PP1 0.710600
7 N7 25.5810 28.3850 37.2780 nh 532 PP1 -0.743600
8 N8 25.4840 31.5120 40.6190 n3 532 PP1 -0.350400
9 C9 24.8030 30.4120 40.4040 c3 532 PP1 0.277400
10 N10 23.8700 27.7270 38.7290 n3 532 PP1 -0.921800
11 C11 23.7730 29.9750 41.3480 c3 532 PP1 -0.026000
12 C12 22.7970 30.8850 41.8090 c3 532 PP1 -0.058700
13 C13 21.8040 30.4670 42.7160 c3 532 PP1 -0.096700
14 C14 21.7780 29.1340 43.1730 c3 532 PP1 -0.061000
15 C15 22.7550 28.2240 42.7220 c3 532 PP1 -0.098700
16 C16 23.7480 28.6430 41.8160 c3 532 PP1 -0.080700
17 C24 20.7120 28.6860 44.1510 c3 532 PP1 -0.064100
18 C28 27.2910 32.7860 39.5450 c3 532 PP1 0.277200
19 C29 27.0910 33.7450 40.7460 c3 532 PP1 -0.105433
20 C33 27.0480 33.5950 38.2550 c3 532 PP1 -0.105433
21 C37 28.7480 32.2800 39.5830 c3 532 PP1 -0.105433
22 H2 27.0700 28.9880 36.0040 h5 532 PP1 0.057800
23 H101 23.6470 26.9570 38.1150 hn 532 PP1 0.439800
24 H102 23.2700 27.8700 39.5280 hn 532 PP1 0.439800
25 H12 22.8060 31.9090 41.4640 hc 532 PP1 0.105700
26 H13 21.0630 31.1740 43.0590 hc 532 PP1 0.095700
27 H15 22.7480 27.2020 43.0720 hc 532 PP1 0.095700
28 H16 24.4970 27.9380 41.4860 hc 532 PP1 0.105700
29 H241 21.0410 28.8660 45.1740 hc 532 PP1 0.046367
30 H242 19.7820 29.2330 43.9880 hc 532 PP1 0.046367
31 H243 20.5020 27.6220 44.0390 hc 532 PP1 0.046367
32 H291 27.7800 34.5890 40.6970 hc 532 PP1 0.052033
33 H292 26.0820 34.1570 40.7700 hc 532 PP1 0.052033
34 H293 27.2710 33.2430 41.6980 hc 532 PP1 0.052033
35 H331 27.6850 34.4800 38.2170 hc 532 PP1 0.052033
36 H332 27.2600 33.0140 37.3580 hc 532 PP1 0.052033
37 H333 26.0130 33.9340 38.1910 hc 532 PP1 0.052033
38 H371 29.4540 33.1110 39.5930 hc 532 PP1 0.052033
39 H372 28.9330 31.6810 40.4750 hc 532 PP1 0.052033
40 H373 28.9920 31.6660 38.7170 hc 532 PP1 0.052033
.<TRIPOS>BOND
1 1 4 1
2 1 8 1
3 1 18 1
4 2 3 2
5 2 7 1
6 2 22 1
7 3 4 1
8 4 5 1
9 4 5 1
10 5 6 1
11 5 9 1
12 6 7 1
13 6 7 1
14 6 10 1
15 8 9 1
16 8 9 1
17 9 11 1
18 10 23 1
19 10 24 1
20 11 12 1
21 11 16 1
22 11 16 1
23 12 13 1
24 12 13 1
25 12 25 1
26 13 14 1
27 13 26 1
28 14 15 1
29 14 15 1
30 14 17 1
31 15 16 1
32 15 27 1
33 16 28 1
34 17 29 1
35 17 30 1
36 17 31 1
37 18 19 1
38 18 20 1
39 18 21 1
40 19 32 1
41 19 33 1
42 19 34 1
43 20 35 1
44 20 36 1
45 20 37 1
46 21 38 1
47 21 39 1
48 21 40 1
.<TRIPOS>SUBSTRUCTURE
1 PP1 1 TEMP 0 **** **** 0 ROOT
To me it looks like the aromatic parts are not recognized.
Any suggestion to solve that problem?
Thank you
Valentina
_______________________________
Valentina Romano | PhD Student |
Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics |
Klingelbergstrasse 61 | CH-4056 Basel |
Phone: +41 61 267 15 80
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Feb 20 2015 - 04:00:03 PST
