On 05/23/2017 12:24 PM, Marcos Villarreal wrote: > I agree with you in principle, but consider the following not uncommon > scenario. We are working on docking (autodock vina) whose score depends on > atom typing. As you know the ligands come in different formats, usually > pdb, mol2 or sdf. We would expect to obtain the same docking result > regardless the input format.
Why? PDB files contain a 3D structure, complete with stereo config (because that's how the crystal structure works). MOL/SDF doesn't have to include 3D coordinates, nor any usable stereo flags. Unless all my MOL/SDFs were generated from PDBs with zero information loss, I wouldn't expect anything from them. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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