ADL: questions for using AutoDock for Virtual Screening

Huang Zunnan zunnanh at
Wed Jan 7 09:48:50 PST 2009

Dear all:

I have a couple of questions for using AutoDock for Virtual Screening:

1) Does anyone have the tutorial for using AutoDock3 for Virtual Screeening.. I tried to download it from AutoDock Website and it always is the tutorial for using AutoDock4 for Virtual Screening.

2) Is it alright if the total charge of the protein or ligand is not an integer in Autodock? 
I am really confused about the charge setting in Autodock.  No matter whether the ligand  (or protein) have all hydrogen atoms added correctly (from CHARMM or other programs), , or have all hydrogen atoms added incorrectly (in Autodock), or have only polar hydrogen atoms added, I always get the protein having Kollman charge and the ligand having Gasteiger charge non-integer. For my research project, I get the protein charge of 6.653e and the ligand charge of -2.501e. Are they reasonable because the non-polar hydrogens have already merged in the protein or the ligand. On the other hand, the real charge of the protein should be 4.0e and that of the ligand should be -1.0e.  

By the way, where we can find the answers to the questions in autodock Archives?

Have a bright 2009!

Zunnan Huang


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