Hi guys,
I have some ligand structures in paper(overall structure). I want to convert those paper structure into pdb.(I have details about the bond order and bond distances).
So can someone can suggest me which is the best open source software to do this (I want to use generated ligand in liganddock application)
There’s a number of programs to do this, but I tend to use Avagadro. It’s available for Windows, Linux, and Mac, and allows you to do structure drawing and simple (e.g. MMFF94) energy minimization of the structures. It can then output structures in either PDB, or perhaps more usefully for Rosetta, in mol and mol2 file formats.
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