I have 3400 files in canonical smiles format and I use "obabel -ismi drug-smiles/* -opdb -O drug-pdb/*.pdb" to convert my SMILES to pdb file. First, is this the correct way of converting? and second, I would like to have the name of the drug included in the pdb file, how should I do that? example:
BALSALAZIDE.smile > O=C(O)CCNC(=O)c1ccc(/N=N/c2ccc(O)c(C(=O)O)c2)cc1 output is: COMPND UNNAMED AUTHOR GENERATED BY OPEN BABEL 3.1.1 HETATM 1 O UNL 1 0.000 0.000 0.000 1.00 0.00 O HETATM 2 C UNL 1 0.000 0.000 0.000 1.00 0.00 C HETATM 3 O UNL 1 0.000 0.000 0.000 1.00 0.00 O HETATM 4 C UNL 1 0.000 0.000 0.000 1.00 0.00 C HETATM 5 C UNL 1 0.000 0.000 0.000 1.00 0.00 C HETATM 6 N UNL 1 0.000 0.000 0.000 1.00 0.00 N HETATM 7 C UNL 1 0.000 0.000 0.000 1.00 0.00 C HETATM 8 O UNL 1 0.000 0.000 0.000 1.00 0.00 O HETATM 9 C UNL 1 0.000 0.000 0.000 1.00 0.00 C HETATM 10 C UNL 1 0.000 0.000 0.000 1.00 0.00 C HETATM 11 C UNL 1 0.000 0.000 0.000 1.00 0.00 C HETATM 12 C UNL 1 0.000 0.000 0.000 1.00 0.00 C HETATM 13 N UNL 1 0.000 0.000 0.000 1.00 0.00 N HETATM 14 N UNL 1 0.000 0.000 0.000 1.00 0.00 N HETATM 15 C UNL 1 0.000 0.000 0.000 1.00 0.00 C HETATM 16 C UNL 1 0.000 0.000 0.000 1.00 0.00 C HETATM 17 C UNL 1 0.000 0.000 0.000 1.00 0.00 C HETATM 18 C UNL 1 0.000 0.000 0.000 1.00 0.00 C HETATM 19 O UNL 1 0.000 0.000 0.000 1.00 0.00 O HETATM 20 C UNL 1 0.000 0.000 0.000 1.00 0.00 C HETATM 21 C UNL 1 0.000 0.000 0.000 1.00 0.00 C HETATM 22 O UNL 1 0.000 0.000 0.000 1.00 0.00 O HETATM 23 O UNL 1 0.000 0.000 0.000 1.00 0.00 O HETATM 24 C UNL 1 0.000 0.000 0.000 1.00 0.00 C HETATM 25 C UNL 1 0.000 0.000 0.000 1.00 0.00 C HETATM 26 C UNL 1 0.000 0.000 0.000 1.00 0.00 C CONECT 1 2 2 CONECT 2 1 1 3 4 CONECT 3 2 CONECT 4 2 5 CONECT 5 4 6 CONECT 6 5 7 CONECT 7 6 8 8 9 CONECT 8 7 7 CONECT 9 7 26 26 10 CONECT 10 9 11 11 CONECT 11 10 10 12 CONECT 12 11 13 25 25 CONECT 13 12 14 14 CONECT 14 13 13 15 CONECT 15 14 24 24 16 CONECT 16 15 17 17 CONECT 17 16 16 18 CONECT 18 17 19 20 20 CONECT 19 18 CONECT 20 18 18 21 24 CONECT 21 20 22 22 23 CONECT 22 21 21 CONECT 23 21 CONECT 24 20 15 15 CONECT 25 12 12 26 CONECT 26 25 9 9 MASTER 0 0 0 0 0 0 0 0 26 0 26 0 END
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
