Hi, currently when I generate conformations with RDKit and want to use them for docking experiments, I have to first rewrite them using the MolConverter node in Knime. I need to do this because some docking software read the information about charges in the atom block rather than in the molecule properties.
Is there a way to specify to SDWriter to write according to the "standard" V2000 format? (1) Here an example with a simple charged molecule (2): MOL1 as created with marvinsketch MOL2 as converted to RDKit format then written with SDWriter MOL3 as rewritten using MolConverter node. If I use MOL2 for docking, some software warn me about valence issues because they cannot read the charge. Did I miss something? Thank you for your help! Cheers, Jose Manuel (1) http://c4.cabrillo.edu/404/ctfile.pdf (2) MOL1 Mrv0541 01051608552D 2 1 0 0 0 0 999 V2000 -0.5728 0.1674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5728 0.9924 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 M CHG 1 2 -1 M END $$$$ MOL2 RDKit 2D 2 1 0 0 0 0 0 0 0 0999 V2000 -0.5728 0.1674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5728 0.9924 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 M CHG 1 2 -1 M END $$$$ MOL3 Mrv0541 01051608552D 2 1 0 0 0 0 999 V2000 -0.5728 0.1674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5728 0.9924 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 M CHG 1 2 -1 M END $$$$ ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
