ADL: autodock Digest, Vol 41, Issue 5

Ying-Ta Wu ywu at
Tue Aug 7 18:48:40 PDT 2007


You should check the manual for atom types used in autodock3.
when a ligand was transferred to pdbq. For example,
Fe-> f
Cl -> c
Br -> b

You need a pdbqtopdb script (find in your $autodock/share) to do the job or 
edit it manually.

Ying-Ta Wu, Ph.D.
GRC, Academia Sinica, Taiwan
phone: 886-2-27899930 ext 345
fax: 886-2-27898811
email:ywu at
----- Original Message ----- 
From: "Daniel Jana" <dfjana at>
To: <autodock at>
Sent: Wednesday, August 08, 2007 3:05 AM
Subject: Re: ADL: autodock Digest, Vol 41, Issue 5

> Mr. Herman Kasro wrote:
>> Dear fellow researchers,
>> I have questions that need your expertise, I hope someone out there could
>> help me.
>> I am using AutoDock 3 in my research.My research is basically about blind
>> docking.
>> So, I have my ligand that is going to be docked to the macromolecule.
>> The ligand that i'm using have a bromine (Br) atom, and I do know why, 
>> after
>> autodocking
>> it changes to "b atom" - so it will be read as Boron instead when I view 
>> and
>> check the [dot]dlg file.
>> My questions:
>> 1. How do I dock a ligand with Bromine and to make sure it gets Bromine 
>> back
>> after docking?
>> 2. Do i need to consider bromine as spare atom types ie X and M?If so, 
>> how I
>> do that?
>> 3.If this question related to the above question, what is the 
>> Lennard-Jones
>> 12-6 parameters for C-Br?
> I do not use Autodock myself so I cannot really go into much detail, but
> I installed the program for a coworker so I know a bit about her problems.
> My best answer for you is to change to Autodock 4. She had the same
> problems as you have, two letter elements were changed to a small letter
> (Br to b, Cl to c, ...) and especially with the maximum number of atoms
> types (which in Autodock 3 was 6). We then found out about the
> availability of Autodock 4 and installed it. All the problems she had
> were easy to solve in this new version. Br and Cl are named Br and Cl,
> the maximum number of atom types was increased and (it seems to me, from
> talks, not from use) that the overall usability of the program increase
> greatly.
> So, if you have no problems in changing the software version I'd
> recommend the new Autodock. You don't even have the problems with the
> license as before...
> Best regards,
> Daniel Jana
> ________________________________________________
> --- ADL: AutoDock List  --- ---

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