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PostPosted: Thu Oct 24, 2013 1:50 pm 
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A colleague sent me some structures to dock and model. I used babel to convert to mol2, then ADT to prepare the .pdbqt file. However, the bonds are completely messed up in the pdbqt. Can anyone lend some assistance or explain what is going on with the pdbqt?


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PostPosted: Tue Oct 29, 2013 4:33 pm 
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Unfortunately, you do not have valid 3-D coordinates for this molecule.
All the z coordinates are 0.0000:

@<TRIPOS>MOLECULE
Proposed-1.cdx
21 22 0 0 0
SMALL
GASTEIGER
****

@<TRIPOS>ATOM
1 O -3.1535 -1.0110 0.0000 O.co2 1 LIG1 -0.2456
2 C -2.4390 -0.5985 0.0000 C.2 1 LIG1 0.3674
3 C -1.7246 -1.0110 0.0000 C.3 1 LIG1 0.1443
4 C -1.0101 -0.5985 0.0000 C.3 1 LIG1 0.1379
5 C -0.2956 -1.0110 0.0000 C.3 1 LIG1 0.0408
6 C 0.4189 -0.5985 0.0000 C.3 1 LIG1 0.0910
7 N 1.8478 -0.5985 0.0000 N.ar 1 LIG1 -0.2738
8 O -2.4390 0.2265 0.0000 O.co2 1 LIG1 -0.2456
9 C -0.5976 0.1160 0.0000 C.3 1 LIG1 0.0335
10 O -1.4226 0.1160 0.0000 O.3 1 LIG1 -0.2251
11 C 1.9340 0.2220 0.0000 C.ar 1 LIG1 0.1013
12 C 2.6015 -0.9340 0.0000 C.ar 1 LIG1 0.0828
13 C 3.1535 -0.3209 0.0000 C.ar 1 LIG1 0.0207
14 C 2.7410 0.3935 0.0000 C.ar 1 LIG1 0.0221
15 C 1.3209 0.7741 0.0000 C.ar 1 LIG1 0.1860
16 N 0.5363 0.5191 0.0000 N.pl3 1 LIG1 -0.1056
17 N 1.4925 1.5810 0.0000 N.ar 1 LIG1 -0.2247
18 C 1.1333 -1.0110 0.0000 C.2 1 LIG1 0.2414
19 O 1.1333 -1.8360 0.0000 O.2 1 LIG1 -0.2716
20 C 2.8902 1.2839 0.0000 C.ar 1 LIG1 0.0223
21 C 2.2771 1.8360 0.0000 C.ar 1 LIG1 0.1005


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PostPosted: Tue Oct 29, 2013 5:18 pm 
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Thanks, funny how obvious it is when someone else points it out. I think I just found a bug in babel.


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PostPosted: Fri Jan 23, 2015 7:21 am 
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Thanks a lot for sharing this valuable information


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