ADL: About Problem of Autodock4, thanks!

mswingle at mswingle at
Wed Oct 17 20:20:25 PDT 2007

I believe you need to download release 4.0.1. I had this same problem with the first release 
of autodock4 (release 4.0.0). This happens because autodock4 combines the information 
from ligand.pdbqt and receptor_flex.pdbqt together during the run. Autodock4 is supposed 
to renumber the atoms in receptor_flex.pdbqt to follow, in sequence, the last atom of 
ligand.pdbqt. However, version 4.0.0 has a bug that prevents this renumbering. Version 
4.0.1 should work. You could also manually fix the receptor_flex.pdbqt file by renumbering 
the atoms to follow the last atom of ligand.pdbqt. That is, if, for example, the last atom in 
ligand.pdbqt is 15, then the first atom in receptor_flex.pdbqt should be 16.

Also, after fixing the numbering problem, if you get an error message about "nested 
branches", you need to upgrade AutoDockTools.



----- Original Message -----
From: ggootc <ggootc at>
Date: Wednesday, October 17, 2007 3:18 pm
Subject: ADL: About Problem of Autodock4, thanks!
To: autodock at

> Dear group of autodock:
>    I am a chinese student in use the autodock4.0, the software is good 
> for me but Ihave found a problem that I can't solve it, please give me 
> some help, thank!
>    I have used ADT to generate the input file that include 5 
> files"receptor_rigid.pdbqt, receptor_flex.pdbqt,  ligand.pdbqr, 
> grid.gdf and par.gpf". WhenI use the flex_docking method to dock a 
> small molecule to receptor in the VMware5.5environment (Red Hat 
> Enterprise linux 4U4), the log file reports error "ATOM and 
> HTMATMrecords must be numbered sequentially from 1" after  the line 
> "Number of atoms inmovable ligand = 14". By check the problem, I have 
> found that when I remove the line of"flexres receptor_flex.pdbqt # 
> file containing flexible residues" in par.dpf, thesoftwate could be 
> runing correctly.
>    How can I do it? The attachment is my 5 input files. Thanks!
> Sincerely: Peng ZhouDepartment of Chemistry, Zhejiang University.   
> ________________________________________________--- ADL: AutoDock List  ---  ---

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