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chandkc / X-ESS

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3D conversion updated mechanism #118

Open chandkc opened 1 year ago

chandkc commented 1 year ago

Convert SDF to PDB -- no geometry optimization and no force field assignment.

  1. obabel -isdf Ganciclovir-d5\ CID_136219948.sdf -opdb -OGan.pdb

  2. Check for 2D in all the input PDBs and SDF converted.

  3. If 2D, Warn User 3b. Do you want to convert to 3D? Yes i. obabel -isdf Ganciclovir-d5\ CID_136219948.sdf -opdb -OGan.pdb --gen3D --minimize --ff GAFF If FASLE ii. obabel -isdf Ganciclovir-d5\ CID_136219948.sdf -opdb -OGan.pdb --gen3D --minimize --ff MMFF94 If FALSE iii. obabel -isdf Ganciclovir-d5\ CID_136219948.sdf -opdb -OGan.pdb --gen3D --minimize --ff gchemical If FASLE iv. obabel -isdf Ganciclovir-d5\ CID_136219948.sdf -opdb -OGan.pdb --gen3D --minimize --ff UFF If FALSE Structure could not be converted to 3D. STOP DOCKING.