ADL: About Problem of Autodock4, thanks!

snoze pa at
Fri Oct 19 09:23:19 PDT 2007

I am unable to get any information where and when autodock uses the
receptor_flex.pdbqt file. Because both dpf and gpf file don't have any
information related to flexible residues though i have created one. Then how
they can use this file to process the flexible residue based docking. Are
you sure that you have receptor_flex.pdbqt  file name in your dpf or gpf
files. If yes please let me know. I posted this question few days back but
didn't get any reply from anyone. I also check the example tutorial in ADT
new version. Though the flexible residue files name are there but not in
neither in gpf nor in dpf files. That will be a great help. thanks

On 10/17/07, mswingle at <mswingle at>
> 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.
> Regards,
> Mark
> ----- 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.
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