Hi, I'm an undergraduate student who is working on the final dissertation, so I'm really new to this type of things and to OpenBabel. I need help to understand if I've done all correctly. I converted a file starting from a SMILES format to obtain a file in mol2 format. For virtual screening with DOCK6.9 I need this file in TRIPOS MOL2 format, but I've read on the documentation that mol2 is SYBYL MOL2 format. Are they the same? For the conversion, I used the command: obabel -i smi inputfile.smi -o mol2 -O outputfile.mol2 --gen3D. I heve another question related to hydrogens atoms: I know that in SMILES format hydrogens are not normally explicitly represented, but I need them in order to perform docking and virtual screening. I didn't write the option -h in the command I used for the conversion, but when I look at the graphic representation of some molecules I see the hydrogens. It seems to me that (even without the -h option) the hydrogens are added explicitly. Is that correct? If someone has already used ZINC15 to download libraries, I have another question: I selected a pH equal to 7.4 before downloading the molecules. So, I didn't use the option -p to add the hydrogens according to physiological pH because I thought the SMILES already contain this information. Is that correct? If someone knows ZINC (even if this is not the help mail for ZINC, but I couldn't find one), does ZINC use canonical SMILES representation? Does the option --gen3D create a reasonable 3D conformation of the molecule, reliable and suitable for docking and virtual screening? Thanks, best regards.
Francesca
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