ADL: Prepare PDB file for AUTODOCK

Lokesh P. Tripathi lokesh at
Thu Oct 18 01:44:15 PDT 2007

Dear all

We are all aware that PDB files need to be processed prior to their use in
AUTODOCK (or for that matter any other docking program). There are plenty
of online resources available for the same.

WHAT IF server has an option to "Prepare PDB file for docking programs",
where the following is carried out for the user uploaded PDB structure (or
"Missing sidechains are modelled in; a small regularisation is performed;
water positions are corrected; symmetry related waters are added;
hydrogens are added if still needed" (Click on
Build/repair/check model --> Prepare PDB file for docking programs)

Suppose I put through my PDB file through this process then does the
refined structure need to be worked with ADT i.e do we still need to do
steps like add hydrogens (WHAT IF does that), merge non-polar hydrogens,
compute gasteiger charges and look for non-integral charges and make them
integral? Or the processing done by WHAT IF alone is sufficient for use in

Many thanks in advance

Lokesh P. Tripathi
National Centre for Biological Sciences,
Bangalore, India

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