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#723 Mistranslation of hydrogens

3.0
open
nobody
File Translation (240)
5
2012-10-23
2011-04-29
Jack
No

Not sure if I'm just clueless or this is a genuine bug, however when converting from cdxml to pdb (for docking modelling basically) I always end up with extra hydrogens being added to my heterocycle. It is cyclam (a tetraazamacrocycle, containing 4 N atoms as part of a ring, each of which bears 1H) and the C-NH-C that is drawn in ChemDraw always ends up as C-NH2-C after converting to pdb.

Any help would be appreciated. Thanks.

Discussion

  • Jack

    Jack - 2011-04-29

    I should add two other things: I tried to just have babel strip all hydrogens, then add the polar ones myself in AutoDockTools. The problems I see with that are: (a) how does babel compute the conformation if it is missing polar hydrogens? and (b) when I readd polar hydrogens in AutoDockTools it adds a polar H to a N=N-C to give N=NH-C which is incorrect.

     

  • Jack

    Jack - 2011-04-29

    Edit: Works fine if I go via SMILES instead of straight from cdxml.

     

  • Chris Morley

    Chris Morley - 2011-04-29

    Could you upload the cdxml file you are having difficulty with? I cannot generate a CDXML file for cyclam because I cannot find any free software that will do this. A cdx file for cyclam made in ChemSketch with explicit H on N and implicit H on C is read ok by openbabel.

     

  • Noel O'Boyle

    Noel O'Boyle - 2012-09-03

    Bump. See comment below.