Here are a few suggestions Changed
#imidazole: note pKa=7.0 #if you uncomment this, also uncomment the seedcharge statement below #TRANSFORM [nD2:1]1c[nH]cc1 >> [n+:1]1c[nH]cc1 7.0 To include N-alkylimidazoles TRANSFORM [nD2:1]1c[nH,#6^3]cc1 >> [n+:1]1c[nH,#6^3]cc1 7.0 #guanidine or amidine #TRANSFORM [#6^2+0:1](~[N^2:2])(~[N^2:3])* >> [#6+:1](~[N:2])(~[N:3])* 12.5 +ve charge on nitrogen not carbon. I +ve charge put on sp3 nitrogen for aesthetic reasons and to avoid potential issues with stereochemistry of C=N bond TRANSFORM [#6^2+0:1](~[N^2:2])(~[N^2:3])* >> [#6:1](~[N:2])(~[N+:3])* 12.5 Added #pyridine TRANSFORM c1cc[nD2:1]cc1 >> c1cc[nH+:1]cc1 5.2 #Phenol TRANSFORM c1ccccc1[OD1-0:1] >> c1ccccc1[O-:1] 10 As Stefano mentioned it is likely that the guanidine or amidine was an error, if you look at the seed charges the for guanidine or amidine the +ve is on the nitrogens. I could add a few more but I thought it would be worth getting some feedback first. Cheers Chris ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
