Dear all, These are the replies received so far:
Daniel Rigden (U. of Liverpool) suggested to do the conversion using https://www.webqc.org/molecularformatsconverter.php . It didn't work for me, the small molecule may be too complex (error message when reading the .mol file);
Petr Kolenko (Czech Technical University in Prague) suggested to use the smiles small molecule definition format. molview.org provides a smiles string in the place where the URL appears when drawing the molecule and then converting it from 2D to 3D.
I located an online smiles translator (https://cactus.nci.nih.gov/translate/ ) and used it to generate a pdb file that appears to satisfy Pymol (see enclosed screen capture). I don't yet know if Pymol will still be happy after docking;
Stephane Rely (ENS Lyon) suggested the use of the prodrg server, and drawing the molecule with JME. I haven't tried this approach yet;
Finally, Massimo Degano (San Raffaele Scientific Institute in Milano) suggested to read in the pdb in Avogadro and writing it out, with CONECT cards written automatically. This didn't work on my system (Avogadro doesn't install due to Qt not being in found at the cmake stage, although it is present on my system)
Thank you for the prompt responses. Fred. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
