# Optimize 3d pdb cannot run haddock

**URL:** <https://ask.bioexcel.eu/t/optimize-3d-pdb-cannot-run-haddock/637>\
**Category:** HADDOCK\
**Created:** [November 25, 2017, 6:25am UTC](https://ask.bioexcel.eu/t/optimize-3d-pdb-cannot-run-haddock/637 "2017-11-25T06:25:27Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![shawnteh1711](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@shawnteh1711](https://ask.bioexcel.eu/u/shawnteh1711)\
**Post date:** [November 25, 2017, 6:25am UTC](https://ask.bioexcel.eu/t/optimize-3d-pdb-cannot-run-haddock/637/1 "2017-11-25T06:25:27Z")

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Previously, I run haddock using ligand extract from bound crystal. However, the docked result is not the same as reference crystal.

So now I try to optimize geometric my 2D structure that I download from pubchem and convert to 3d using avagadro. However the pdb produce missing some column, and cannot submit to Haddock for docking.

There I would like to know is it correct for me to just extract the ligand from bound crystal? Do I need to do any refinement? And is there a way to convert 2D to 3D without the missing column in PDB? Would appreciate if anyone can kindly advice.

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [November 26, 2017, 4:14pm UTC](https://ask.bioexcel.eu/t/optimize-3d-pdb-cannot-run-haddock/637/2 "2017-11-26T16:14:22Z")

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In terms of conversion from smile to 3D, we like the omega toolkit from OpenEye (free for academics). But there are indeed other solutions.