ADL: autodock Digest, Vol 62, Issue 5

hamed ali hamed_ali37 at yahoo.com
Mon Oct 12 12:26:27 PDT 2009


Dear all 
hope you all are fine
Please I am looking for phython version 2.5 for Winwows visa
please if any one have that version send me
thanks in advance
 weasslamo alikom
yours
Hamed Ismail ali




--- On Mon, 10/12/09, autodock-request at scripps.edu <autodock-request at scripps.edu> wrote:


From: autodock-request at scripps.edu <autodock-request at scripps.edu>
Subject: autodock Digest, Vol 62, Issue 5
To: autodock at scripps.edu
Date: Monday, October 12, 2009, 3:00 PM


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Today's Topics:

   1.  AutoDock/Vina Performance (Nancy)
   2. Re:  AutoDock/Vina Performance (Nancy)
   3.  AutoDock Vina Viewing Results (Nancy)
   4. Re:  ImportError: /lib/libgcc_s.so.1: version `GCC_3.3' not
      found (Nicolas Sapay)


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

Message: 1
Date: Sun, 11 Oct 2009 15:14:31 -0400
From: Nancy <nancy5villa at gmail.com>
Subject: ADL: AutoDock/Vina Performance
To: autodock at scripps.edu
Message-ID:
    <765a9fbb0910111214u17024224sd889f03d8f6a7077 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hello,

I am new to AutoDock (and AutoDock Vina), and I am attempting to perform
virtual screening using AutoDock 4.2 (and Vina).

I ran a "blind docking" simulation using Vina by enlarging the box to cover
the entire protein, and also ran a docking simulation using a smaller box
that only covered the binding pocket.  I noticed that the performance did
not increase significantly when using a smaller box.  Does this mean that
when using a smaller box there is more detail in the docking simulation?

As it takes several minutes to perform a docking simulation with Vina on a
single CPU (at exhaustiveness 8), I am wondering if there is a way to
increase the performance in order to accelerate virtual screening of large
libraries (>10,000 compounds).

Thank you.

Nancy


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

Message: 2
Date: Sun, 11 Oct 2009 15:55:41 -0400
From: Nancy <nancy5villa at gmail.com>
Subject: Re: ADL: AutoDock/Vina Performance
To: autodock at scripps.edu
Message-ID:
    <765a9fbb0910111255uddf2177vbecd9697f91d7fc0 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hello,

I have used the FlexX program for docking before, and it takes less than a
minute to dock a compound on a single CPU; does AutoDock/Vina perform
docking in a more comprehensive manner, thus taking more time?

Also, is there any particular hardware configuration setup (preferable a
single computer) that is optimal for running AutoDock/Vina (is there any way
to accelerate Vina on a GPU as well)?

Thanks,

Nancy



On Sun, Oct 11, 2009 at 3:33 PM, Wim Nerinckx <wimnerinckx at lavabit.com>wrote:

> Dear Nancy,
>
> Speed in Vina (as well as in AutoDock) depends heavily on the amount of
> rotatables in ligand and receptor. You may try some test-screens with say
> only 20 compounds to see if decreasing exhaustiveness to 4, and setting less
> rotatables in the receptor, makes a significant difference. I recently ran a
> 10.000 screen with Vina on exhaustiveness 4, with only one side-chain
> residue of the receptor as flexible; this was finished in less than a week
> on a linux octacore, and then I re-ran the 50 best on exhaustiveness 16 to
> get my final result - which hardly differed from the original 50. See some
> more info in the Vina forum at:
>
> http://mgl.scripps.edu/forum/viewtopic.php
> ?f=12&t=235&sid=edf9a8fb4060e6bbeb6e87eca2d72add
>
> Greetings,
> WIM, Belgium
>
>
>
> On 11 Oct 2009, at 21:14, Nancy wrote:
>
>  Hello,
>>
>> I am new to AutoDock (and AutoDock Vina), and I am attempting to perform
>> virtual screening using AutoDock 4.2 (and Vina).
>>
>> I ran a "blind docking" simulation using Vina by enlarging the box to
>> cover
>> the entire protein, and also ran a docking simulation using a smaller box
>> that only covered the binding pocket.  I noticed that the performance did
>> not increase significantly when using a smaller box.  Does this mean that
>> when using a smaller box there is more detail in the docking simulation?
>>
>> As it takes several minutes to perform a docking simulation with Vina on a
>> single CPU (at exhaustiveness 8), I am wondering if there is a way to
>> increase the performance in order to accelerate virtual screening of large
>> libraries (>10,000 compounds).
>>
>> Thank you.
>>
>> Nancy
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>
>
>
>


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

Message: 3
Date: Sun, 11 Oct 2009 17:41:51 -0400
From: Nancy <nancy5villa at gmail.com>
Subject: ADL: AutoDock Vina Viewing Results
To: AutoDock Users <autodock at scripps.edu>
Message-ID:
    <765a9fbb0910111441s3f83122bk1d85b22a2f5d305e at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hello,

After a docking run using Vina, when I try to view the results in
AutoDockTools by clicking on "Analyze -> Dockings -> Open AutoDock vina
result..." and I choose "Single molecule with multiple conformations", I
receive the following error message (from the python shell):

=====================================================

>>> ERROR *********************************************
Traceback (most recent call last):
  File
"/usr/local/MGLTools-1.5.4/MGLToolsPckgs/Updates/tested/ViewerFramework/VF.py",
line 735, in tryto
    result = apply( command, args, kw )
TypeError: doit() got an unexpected keyword argument 'modelsAs'
ERROR *********************************************
Traceback (most recent call last):
  File
"/usr/local/MGLTools-1.5.4/MGLToolsPckgs/Updates/tested/ViewerFramework/VF.py",
line 735, in tryto
    result = apply( command, args, kw )
  File
"/usr/local/MGLTools-1.5.4/MGLToolsPckgs/Updates/tested/AutoDockTools/autoanalyzeCommands.py",
line 3061, in doit
    mols.current_index = 0
AttributeError: 'str' object has no attribute 'current_index'

=====================================================


Also, as another question, I have used the FlexX program for docking before,
and it takes less than a minute to dock a compound on a single CPU; does
AutoDock/Vina perform docking in a more comprehensive manner, thus taking
more time?  Is there any particular single computer/small cluster hardware
configuration setup that is optimal for running AutoDock/Vina (is there any
way to accelerate Vina on a GPU as well)?

Thanks,

Nancy


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

Message: 4
Date: Mon, 12 Oct 2009 10:30:34 +0200
From: Nicolas Sapay <nicolas.sapay at cermav.cnrs.fr>
Subject: Re: ADL: ImportError: /lib/libgcc_s.so.1: version `GCC_3.3'
    not    found
To: autodock at scripps.edu
Message-ID: <4AD2E92A.6000709 at cermav.cnrs.fr>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"

Hello Harpreet,

harry rajput a ?crit :
> Hi,
>
> while trying running autodock tools (ADT) on my Redhat Linux machine.
> It go the error
>
> "ImportError: /lib/libgcc_s.so.1: version `GCC_3.3' not found
> (required by /usr/local/bin/lib/libstdc++.so.5)"
>   
This probably indicates that GCC 3 is not correctly  installed on your 
system, or at least is not in a regular location. You can check the 
version of the GNU compiler with the following command:

    gcc -dumpversion

I recommend you to install GCC 3 with a package manager like yum or rpm.

> Details of the run are as given below: -
> [root at localhost bin]# ./adt
> setting PYTHONHOME environment
> Run AutoDockTools from /usr/local/bin/MGLToolsPckgs/AutoDockTools
> Traceback (most recent call last):
>   File "/usr/local/bin/MGLToolsPckgs/AutoDockTools/__init__.py", line
> 370, in runADT
>     from Pmv.moleculeViewer import MoleculeViewer
>   File "/usr/local/bin/MGLToolsPckgs/Pmv/moleculeViewer.py", line 20,
> in <module>
>     from DejaVu.Geom import Geom
>   File "/usr/local/bin/MGLToolsPckgs/DejaVu/__init__.py", line 181, in <module>
>     from Viewer import Viewer
>   File "/usr/local/bin/MGLToolsPckgs/DejaVu/Viewer.py", line 45, in <module>
>     from opengltk.OpenGL import GL
>   File "/usr/local/bin/MGLToolsPckgs/opengltk/OpenGL/GL.py", line 7,
> in <module>    from opengltk.extent._gllib import *
> ImportError: /lib/libgcc_s.so.1: version `GCC_3.3' not found (required
> by /usr/local/bin/lib/libstdc++.so.5)
> hit enter to continue
>
> Thanks
> Harpreet
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>   
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