Hello,
I'm new to OpenBabel and generally to small molecule analysis.
I want to dock some small molecule (trisporic acid) to some receptor
protein.
Docking software only accepts small molecule in Mol2 format.
I could not found trisporic acid in public databases, only found it in
Pubchem.
In PubChem i can download molecule in 3 formats: ASN, XML and SDF
OpenBabel can convert from Pubchem format (*.pc) to Mol2.
I dont know what is exact *pc format, but i tried all 3 above formats,
(I also used XML and SDF formats)
but OpenBabel always give some warning, like does not recognizing some
atoms,
and consequently docking software does not accept Mol2 format created by
OpenBabel because something wrong in topology.
Could someone please give me some advise, what I'm doing wrong
and what maybe possible solution.
Thanks in advance,
Asaf
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