ADL: autodock Digest, Vol 48, Issue 37

jose correa corrjose at
Wed Mar 26 13:38:37 PDT 2008

hay que darle prosa, hay gente trabajando docking sobre este receptor, haber
si te inscribes al firo de autodock.

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From: autodock-request at <autodock-request at>
Date: 26-mar-2008 13:00
Subject: autodock Digest, Vol 48, Issue 37
To: autodock at

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Today's Topics:

  1.  Trouble with viewing interactions..!!! (namita at
  2.  error message in autodock4 (Borries Demeler)
  3.  (no subject) (qiaoyan)
  4. Re:  (no subject) (Bobby Barnett)


Message: 1
Date: Wed, 26 Mar 2008 14:59:08 +0530 (IST)
From: namita at
Subject: ADL: Trouble with viewing interactions..!!!
To: autodock at
Message-ID: <56563. at>
Content-Type: text/plain;charset=iso-8859-1

Hi All

Thanks everyone for responding to the queries.
I have one more doubt. Every time i finish the whole of the docking
procedure, I try to view the interactions between the ligand and the
(Analyze -> Docking -> Show interactions)

But it opens up a Python shell window and shows me the following errors...

File "/usr/local/MGLTools-1.4.6/MGLToolsPckgs/ViewerFramework/", line
714, in tryto
   result = apply( command, args, kw )
line 1922, in doit
line 1759, in build
   self.intDescr = InteractionDescriptor(lig, macro, percentCutoff)
line 44, in __init__
line 51, in build
   self.buildHydrogenBonds()           #
line 117, in buildHydrogenBonds
   lig_gly_res = d['lig_hb_gly_res'] = lig_hb_res.get(lambda x:
UnboundLocalError: local variable 'lig_hb_res' referenced before assignment

Could anyone please help me fix these errors. I tried changing the Grid
and Docking parameters. But its of no help.

Thanks in advance


Message: 2
Date: Wed, 26 Mar 2008 06:53:49 -0600 (CST)
From: Borries Demeler <demeler at>
Subject: ADL: error message in autodock4
To: autodock at
Cc: yat at
Message-ID: <200803261253.m2QCrnQq032219 at>
Content-Type: text/plain; charset=us-ascii


I didn't search your archives to see if this was mentioned before,
but I didn't see it listed in your faqs...

When screening a large library autodock4 fails to converge in
about 0.5% of the compounds listed. In those cases, I see the

NOTE: All energies are equal in population; re-initializing....

endlessly repeated in the log file, which grows very large. I am not
sure if this is a bug in the initialization, but in my opinion the
program should exit in such a case more gracefully. I never see this
string in any of successful fits, which would indicate to me that
the program has hit en error condition from which it can't escape.
So my suggestion would be to better deal with the initialization, or
change the output message to better reflect the true error condition,
whatever it is.

I should also mention that some of the compounds miraculously do
converge if I just restart the program. I don't know how the program
works, but my interpretation of this symptom would be that you use
time to initialize the random seed of your GA, and then when I restart
it I get a better initialization. However, when the program gets stuck
in this loop, even though it says that it reinitializes, it never actually
does. Does that seem plausible?

Thanks, -Borries


Message: 3
Date: Wed, 26 Mar 2008 21:01:48 +0800
From: "qiaoyan" <qiaoyan at>
Subject: ADL: (no subject)
To: <autodock at>
Message-ID: <200803261301.m2QD1lcH010718 at>
Content-Type: text/plain;       charset="us-ascii"

Hi everybody
> During the flexible docking procedure I was checking the docking log
> console and I met numerous "infinite energy" messages. I suppose that
> it means that the final docking energy is way to high (or low in my
> case) and that spoils the entire docking procedure. Anyway, I wonder
> if any of you had similar issue with autodock4, and if you had how did
> you solve the problem .thank you very much.


Message: 4
Date: Wed, 26 Mar 2008 14:08:50 -0400 (EDT)
From: Bobby Barnett <bobby.barnett at>
Subject: Re: ADL: (no subject)
To: autodock at
Message-ID: <20080326140850.AXV00178 at>
Content-Type: text/plain; charset=us-ascii


I thought I would point out that 2I35 is a low resolution rhodopsin
structure.  The beta2-adrenergic receptor file is 2RH1 with the T4 lysozyme
structure.  You can remove the residues from 1002 to 1161 to eliminate the
inserted protein.  Many GPCR structures are built without knowing the exact
loop structures.

Bobby Barnett

---- Original message ----
>Date: Wed, 26 Mar 2008 15:26:30 +0800
>From: "qiaoyan" <qiaoyan at>
>Subject: ADL: (no subject)
>To: <autodock at>
>I am now working on a GPCR system as part of my bachelor's degree. Now the
>crystal structure of beta2-adrenergic receptor can be accessed, which PDB
>is 2I35 in <> . But in 2I35, the
>third internal loop is substituted by T4L protein in order to achieve a
>better crystallization.I wang to remove the T4L.let the    the protein with
>the absence of the third loop to dock to the carazolol-a partial inverse
>anatagonist.there is an error:autogrid4.warning:Found an H bonding atom
>thre  bonded atoms,atom series nunmber 676.
>Another question:how big the grid box should be ?when I use the intergal
>protein,everything went fine until it begin to dock,
>  ERROR!  energy is infinite!I don't understand why,please help
>me.thank you for your attention.
>--- ADL: AutoDock List  --- ---
Bobby L. Barnett PhD
Department of Chemistry
University of Cincinnati
PO Box 210172
301 Clifton Court
Cincinnati, OH 45221-0172
Phone:(513)556-9230 Lab:(513)556-9214


--- ADL: AutoDock List  --- ---

End of autodock Digest, Vol 48, Issue 37

Ph.D. JOSE CORREA BASURTO Professor of Pharmacology, Department of
Biochemistry and Pharmacology, Escuela Superior de Medicina, Instituto
Politécnico Nacional, México. Plan de San Luis Y diaz Mirón S/N, Col. Casco
de Santo Tomas, Mexico city, México. CP: 11340. Tel/Fax; (+5255) 57296000
Ext 62747 and 62767 e:mail: josecorreabasurto at or jcorreab at,
corrjose at

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