ADL: autodock Digest, Vol 62, Issue 2

Yasmine yasmine_moemen at yahoo.com
Mon Oct 5 12:26:42 PDT 2009


hi Mr kumar
to dock your ligand in a specific binding site , in gpf file;  change your grid center fromauto to the coordinates of your binding site.
as you know you should have your ligand and receptor in pdbqt then you prepare your grid parameter file(GPF) and your DPF
for more information you should read the manual of autodock version 4

Best regards
Yasmine
M.Sc. in physical chemistry
Egypt




________________________________
From: "autodock-request at scripps.edu" <autodock-request at scripps.edu>
To: autodock at scripps.edu
Sent: Monday, October 5, 2009 9:00:01 PM
Subject: autodock Digest, Vol 62, Issue 2

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Today's Topics:

   1.  Share your view (naga vignesh)
   2.  autodock4 installation in mac os x system (andrew silvanus)
   3. Re:  autodock4 installation in mac os x system (Folmer Fredslund)
   4.  solving ValueError: invalid literal for float() Re: Reading
      .dlg file bombs out (M. Shahid)
   5.  Docking of ligand in a particular pose (Vikash kumar)
   6. Re:  Docking of ligand in a particular pose (Laura Lowe Furge)


----------------------------------------------------------------------

Message: 1
Date: Sun, 4 Oct 2009 21:01:03 -0700
From: naga vignesh <naga.vignesh at gmail.com>
Subject: ADL: Share your view
To: autodock at scripps.edu
Message-ID:
    <b1a100700910042101u79ac02ei38a2d01adc4c4862 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Dear Sir/Madam ,


    I have prepared few questions about docking software.I need your support
on this issue. So, please all of you  answer this questions.

1.Can you list out the known commercial and Open Source softwares for
docking?.

2. What are the docking softwares (commercial/open source) you are using?
3.Is there any specific reason for using that software?

4.How many hours it is needed to do minimum 100 dockings? Or any rough idea
on that with your docking software.

5.Do you think, reducing the processing time is needed in your software?

6. Your name and designation?

Thanks for spending your valuable time to answer the questions.

-- 
with regards
s.naga vignesh


Give to the world, good you have;
You will get best  what it has.


------------------------------

Message: 2
Date: Mon, 5 Oct 2009 13:01:27 +0530
From: andrew silvanus <milvangene at gmail.com>
Subject: ADL: autodock4 installation in mac os x system
To: autodock at scripps.edu
Message-ID:
    <eae2c4590910050031t6abfc112v526526c9f9ac660 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hello sir/madam,
                       i am andrew silvanus.i am preferring to use auto dock
4 for my project purposes ,as i am not too familiar with commands regarding
the installation through mac os terminal. i request you to furnish every
possible information regarding complete information of installation of
autodock 4 in mac os.

thank you

yours sincerly

andrew silvanus.a


------------------------------

Message: 3
Date: Mon, 5 Oct 2009 10:01:58 +0200
From: Folmer Fredslund <folmerf at gmail.com>
Subject: Re: ADL: autodock4 installation in mac os x system
To: autodock at scripps.edu
Message-ID:
    <991070400910050101qce66363gdeaaf1afa0ebbd4f at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Dear Andrew,

2009/10/5 andrew silvanus <milvangene at gmail.com>:
> Hello sir/madam,
> ? ? ? ? ? ? ? ? ? ? ? i am andrew silvanus.i am preferring to use auto dock
> 4 for my project purposes ,as i am not too familiar with commands regarding
> the installation through mac os terminal. i request you to furnish every
> possible information regarding complete information of installation of
> autodock 4 in mac os.
>


I am not a super-user of the AutoDock software of some sorts, but I
think it is generally advisable to look at the help section of the
software you try to install.

I just did a web-search for:
auto dock 4 install mac

on google.com and found this site as the first hit.
http://autodock.scripps.edu/faqs-help/faq/how-do-i-install-autodock-on-linux-and-mac-os-x

As mentioned I am no super-user, but please try to follow these
guidelines for installation.



Best regards,
Folmer Fredslund, PhD



------------------------------

Message: 4
Date: Mon, 5 Oct 2009 12:15:31 +0200
From: "M. Shahid" <mohammad.shahid at gmail.com>
Subject: ADL: solving ValueError: invalid literal for float() Re:
    Reading    .dlg file bombs out
To: autodock at scripps.edu
Message-ID:
    <3680fa180910050315l50be35eaof922adb7f3e98c42 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi,

I also encounterd the same problem and did a quick tracking into the problem
and found a workaround as below:

This error (ValueError: invalid literal for float() ) comes when we use
prepare_dpf42.py
and AutoDock 4.2 Release 4.2.2.1 produces the following line in the result
dlg file
DOCKED: USER    (4) Unbound System's Energy  [=(2)] = ......

while the earlier version of AD produces the line
DOCKED: USER    (4) Unbound System's Energy    = .....

In the DlgParser.py script in
(~/MGLTools-1.5.4/MGLToolsPckgs/AutoDockTools/DlgParser.py)

add these lines:

           elif find(l, "(4) Unbound System's Energy  [=(2)]")>-1:
                #USER    (4) Unbound System's Energy         =   -0.85
kcal/mol
                d['unbound_energy'] = float((ll)[7])

before these lines:

            elif find(l, "(4) Unbound System's Energy")>-1:
                #USER    (4) Unbound System's Energy         =   -0.85
kcal/mol
                d['unbound_energy'] = float((ll)[6])


Please make indentations of the above lines similar to the later lines
(python requirements of correct indentations).

After the above changes now the dlg file can be opened without that
ValueError in MGLTools
or the dlg results can be summarized by the script summarize_results4.py
script.

Please refere to the Autodock parameters details for further information at
http://autodock.scripps.edu/resources/parameters

Best regards,

--
Shahid.


On Tue, Sep 29, 2009 at 3:09 AM, Dean Cuebas
<deancuebas at missouristate.edu>wrote:

> Dear colleagues,
>
> Things were working fine, dockings, analysis, etc... now for some reason
> analysis is impossible.
>
> I?ve done some dockings that seem to work correctly, and finish the docking
> with no error.
>
> But when I go to analyze the docking with my .dlg file I get:
>
> ERROR *********************************************
> Traceback (most recent call last):
>  File "/Library/MGLTools/1.5.4/MGLToolsPckgs/ViewerFramework/VF.py", line
> 735, in tryto
>    result = apply( command, args, kw )
>  File
>
> "/Library/MGLTools/1.5.4/MGLToolsPckgs/AutoDockTools/autoanalyzeCommands.py"
> , line 2848, in doit
>    d.readDlg(dlgFile)
>  File "/Library/MGLTools/1.5.4/MGLToolsPckgs/AutoDockTools/Docking.py",
> line 74, in readDlg
>    dlo = DockingLogObject(self, dlgFile)
>  File "/Library/MGLTools/1.5.4/MGLToolsPckgs/AutoDockTools/Docking.py",
> line 337, in __init__
>    parser.parse(filename)
>  File "/Library/MGLTools/1.5.4/MGLToolsPckgs/AutoDockTools/DlgParser.py",
> line 106, in parse
>    self.match(allLines)
>  File "/Library/MGLTools/1.5.4/MGLToolsPckgs/AutoDockTools/DlgParser.py",
> line 219, in match
>    apply(d['func'], (lines,), {})
>  File "/Library/MGLTools/1.5.4/MGLToolsPckgs/AutoDockTools/DlgParser.py",
> line 696, in getModelLines
>    self.makeModels(modelList)
>  File "/Library/MGLTools/1.5.4/MGLToolsPckgs/AutoDockTools/DlgParser.py",
> line 792, in makeModels
>    clist.append(self.makeModel(curMod))
>  File "/Library/MGLTools/1.5.4/MGLToolsPckgs/AutoDockTools/DlgParser.py",
> line 886, in makeModel
>    d['unbound_energy'] = float((ll)[6])
> ValueError: invalid literal for float(): =
>
> Any suggestions would be appreciated.  I reinstalled MGL, etc...., nothing
> that I do seems to help.
> Thanks so much in advance!!!
>
> Dr. C
> Dr. Dean Cuebas, Associate Prof of Chemistry
> deancuebas at missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
> Dept. of Chemistry, Missouri State University
> Springfield, Missouri 65897
>
>
> "It was pretty good. Even the music was nice."
>
> Yogi Berra, after attending an opera
>
>
>
> > From: "autodock-request at scripps.edu" <autodock-request at scripps.edu>
> > Reply-To: "autodock at scripps.edu" <autodock at scripps.edu>
> > Date: Mon, 28 Sep 2009 14:00:01 -0500
> > To: "autodock at scripps.edu" <autodock at scripps.edu>
> > Subject: autodock Digest, Vol 61, Issue 25
> >
> > Send autodock mailing list submissions to
> > autodock at scripps.edu
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://mgldev.scripps.edu/mailman/listinfo/autodock
> > or, via email, send a message with subject or body 'help' to
> > autodock-request at scripps.edu
> >
> > You can reach the person managing the list at
> > autodock-owner at scripps.edu
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of autodock digest..."
>
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>


------------------------------

Message: 5
Date: Mon, 5 Oct 2009 11:11:48 +0530
From: "Vikash kumar" <kvikash01 at gmail.com>
Subject: ADL: Docking of ligand in a particular pose
To: autodock at scripps.edu
Message-ID: <1f109fe4909c4075750856d2687000c8.squirrel at gpo.iitb.ac.in>
Content-Type: text/plain;charset=utf-8

Hi All

I want to dock the ligand in a particular binding site and in a particular
orientation. Because binding mode of the same ligand in different protein
is known. Anyone please guide me how to do this by using AutoDock 4. Any
help will be highly appreciated.

--
Thanks
With Regards

Biotechnology
School of Biosciences & Bioengg.
IIT Bombay
Powai
Mumbai-400076
India
Contact no. 09819442221


------------------------------

Message: 6
Date: Mon, 5 Oct 2009 14:29:31 -0400
From: Laura Lowe Furge <lfurge at sbcglobal.net>
Subject: Re: ADL: Docking of ligand in a particular pose
To: "autodock at scripps.edu" <autodock at scripps.edu>
Message-ID: <BE49FDDC-7635-49DD-82F2-3E09F5BDFAD5 at sbcglobal.net>
Content-Type: text/plain;    charset=UTF-8;    delsp=yes;    format=flowed

Here are some "in house" directions my lab uses, Good luck,
LLF

??????


On Oct 5, 2009, at 1:41 AM, Vikash kumar wrote:

> Hi All
>
> I want to dock the ligand in a particular binding site and in a  
> particular
> orientation. Because binding mode of the same ligand in different  
> protein
> is known. Anyone please guide me how to do this by using AutoDock  
> 4. Any
> help will be highly appreciated.
>
> --
> Thanks
> With Regards
>
> Biotechnology
> School of Biosciences & Bioengg.
> IIT Bombay
> Powai
> Mumbai-400076
> India
> Contact no. 09819442221
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/ 
> mailing_list ---



Laura Lowe Furge, Ph.D.
Associate Professor
Department of Chemistry
Kalamazoo College
1200 Academy Street
Kalamazoo, MI 49080

Phone: 269-337-7020
FAX: 269-337-7251
email: lfurge at kzoo.edu






------------------------------

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--- ADL: AutoDock List  --- http://www.scripps.edu/pub/olson-web/doc/autodock/ ---

End of autodock Digest, Vol 62, Issue 2
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