ADL: Ligands and Hydrogens (Khaled)

Bagdevi bagdevi.mishra at gmail.com
Wed Jun 24 23:16:03 PDT 2009


Yes, this result will be different from the previous one.


Regards,
Bagdevi Mishra.



On Thu, Jun 25, 2009 at 11:09 AM, <kbarakat at ualberta.ca> wrote:

> Thanks a lot Bagdevi for your reply,
>
> It works fine now. However, I am wondering if this alternative prepartion
> can affect my docking results and make it different from the previous one
> where non-polar hydrogens were merged?
>
> Khaled
>
>
>
> Quoting autodock-request at scripps.edu:
>
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>> Today's Topics:
>>
>>   1.  vina virtual screening result? (venkat)
>>   2.  Ligands and hydrogens (kbarakat at ualberta.ca)
>>   3.  Ligands and Hydrogens (kbarakat at ualberta.ca)
>>   4.  for registration (rachit raj)
>>   5. Re:  Ligands and Hydrogens (Bagdevi)
>>   6.  maximum number of map (Alessandro Contini)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Tue, 23 Jun 2009 12:36:18 -0700 (PDT)
>> From: venkat <vkabas at yahoo.com>
>> Subject: ADL: vina virtual screening result?
>> To: autodock at scripps.edu
>> Message-ID: <650582.89399.qm at web34301.mail.mud.yahoo.com>
>> Content-Type: text/plain; charset=us-ascii
>>
>>
>> Hey
>>
>> I did run vina for virtual screening.
>>
>> Is it any script that can be useful extract the best result pdbqt.
>> Other words, any way to check quickly which ligand has lowest
>> binding energy and how can I get pdbqt from entire data base of ligand
>> pdbqt.
>>
>> Thanks
>> venkat
>>
>> --- On Mon, 6/22/09, Sargis Dallakyan <sargis at scripps.edu> wrote:
>>
>>  From: Sargis Dallakyan <sargis at scripps.edu>
>>> Subject: Re: ADL: Error loading AutoDock Tools
>>> To: autodock at scripps.edu
>>> Date: Monday, June 22, 2009, 1:25 PM
>>> Hassan Thomas Mamdani wrote:
>>> > Hi All
>>> >
>>> > I wonder if anyone has encountered the following error
>>> when loading ADT,
>>> > and if so what did they do to resolve the issue.
>>> >
>>> >
>>> > M:\Notebooks\NB4\04htm53\pH3>adt
>>> >
>>> > M:\Notebooks\NB4\04htm53\pH3>set
>>> MGLPYTHONPATH=C:\Program Files\MGLTools
>>> > 1.5.4
>>> >
>>> >
>>> M:\Notebooks\NB4\04htm53\pH3>"C:\Python25\python.exe"
>>> "C:\Program
>>> > Files\MGLTools 1.5.4\MGLTools
>>> > Pckgs\AutoDockTools\bin\runAdt.py"
>>> > Run AutoDockTools from C:\Program Files\MGLTools
>>> > 1.5.4\MGLToolsPckgs\AutoDockTools
>>> > DLL load failed: The specified module could not be
>>> found.
>>> > Resource file used to customize PMV:
>>> M:\\.mgltools\1.5.4\Pmv\_pmvrc
>>> > Traceback (most recent call last):
>>> >   File "C:\Program Files\MGLTools
>>> > 1.5.4\MGLToolsPckgs\AutoDockTools\__init__.py", line
>>> 373, in
>>> > runADT
>>> >     title=title, withShell= not
>>> interactive, verbose=False)
>>> >   File "C:\Program Files\MGLTools
>>> > 1.5.4\MGLToolsPckgs\Pmv\moleculeViewer.py", line 315,
>>> in __in
>>> > it__
>>> >     verbose=verbose,
>>> trapExceptions=trapExceptions)
>>> >   File "C:\Program Files\MGLTools
>>> > 1.5.4\MGLToolsPckgs\ViewerFramework\VF.py", line 345,
>>> in __in
>>> > it__
>>> >     verbose=verbose)
>>> >   File "C:\Program Files\MGLTools
>>> > 1.5.4\MGLToolsPckgs\ViewerFramework\VFGUI.py", line
>>> 270, in _
>>> > _init__
>>> >     cnf = {"addScenarioButton":
>>> False})
>>> >   File "C:\Program Files\MGLTools
>>> 1.5.4\MGLToolsPckgs\DejaVu\Viewer.py",
>>> > line 719, in __init__
>>> >     master=guiMaster)
>>> >   File "C:\Program Files\MGLTools
>>> > 1.5.4\MGLToolsPckgs\DejaVu\ViewerGUI.py", line 433, in
>>> __init
>>> > __
>>> >     self.tvolist =
>>> TreeView(master=self.ObjectListFrame,displayValue=True)
>>> >   File "C:\Program Files\MGLTools
>>> >
>>> 1.5.4\MGLToolsPckgs\mglutil\gui\BasicWidgets\Tk\TreeWidget\tr
>>> > ee.py", line 1581, in __init__
>>> >     self.plus_icon  =
>>> ImageTk.PhotoImage( master=master,image=plus_icon)
>>> >   File "C:\Program Files\MGLTools
>>> 1.5.4\MGLToolsPckgs\PIL\ImageTk.py",
>>> > line 116, in __init__
>>> >     self.paste(image)
>>> >   File "C:\Program Files\MGLTools
>>> 1.5.4\MGLToolsPckgs\PIL\ImageTk.py",
>>> > line 181, in paste
>>> >     import _imagingtk
>>> > ImportError: DLL load failed: The specified module
>>> could not be found.
>>> > hit enter to continue
>>> >
>>> > When I hit enter the splash screen vanishes and the
>>> program exits.  I'm
>>> > running on Windows XP and have just seen the error
>>> after successfully
>>> > using ADT for a couple of years.  I recently
>>> changed my own Python
>>> > installation to ActivePython and have loaded GTK in
>>> order to use another
>>> > bit of code.  Would that have anything to do with
>>> the problem?
>>>
>>> Thank you for your message. We are using Python Imaging
>>> Library (PIL) 1.1.5 which is a third part package that we
>>> did not change for a long time:
>>> http://www.pythonware.com/products/pil/index.htm
>>>
>>> In order to troubleshoot this problem I'd like to know if
>>> one of our earlier releases, 1.5.2 for instance, works with
>>> your current configuration:
>>> http://mgltools.scripps.edu/downloads/previous-releases/mgltools-1-5.2
>>>
>>> Also, if you use Python 2.5 from python.org instead of
>>> ActivePython does this problem persists?
>>>
>>> Thank you,
>>> Sargis
>>>
>>>
>>> --
>>> Sargis Dallakyan, Ph.D. - Research Programmer III
>>> The Scripps Research Institute,
>>> Dept. Molecular Biology,  MB-5,
>>> 10550  North Torrey Pines Road,
>>> La Jolla,  CA 92037-1000
>>> Tel: (858) 784-9559
>>> http://mgltools.scripps.edu/Members/sargis
>>> ________________________________________________
>>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
>>> ---
>>>
>>>
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Tue, 23 Jun 2009 16:13:23 -0600
>> From: kbarakat at ualberta.ca
>> Subject: ADL: Ligands and hydrogens
>> To: autodock at scripps.edu
>> Message-ID: <20090623161323.691559cvb99r7hk4 at webmail.ualberta.ca>
>> Content-Type: text/plain;       charset=ISO-8859-1;     DelSp="Yes";
>>        format="flowed"
>>
>> Hi
>>
>> Is there a way to keep all hydrogens in the ligand.pdbqt files and not
>> to merge non-polar hydrogens. My plan is to use Molecular Dynamics
>> simulations to calculate the binding energies of several
>> Receptor-Ligand complex starting from the proposed docked structures.
>> My major problem in that is: AutoDock merge the hydrogens of the
>> ligand and it's very hard to track them back to the initial
>> protonation states even with programs like open babel.
>>
>> Thanks for your time and your help is so much appreciated
>>
>> With my best regards
>> Khaled
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Tue, 23 Jun 2009 20:10:52 -0600
>> From: kbarakat at ualberta.ca
>> Subject: ADL: Ligands and Hydrogens
>> To: autodock at scripps.edu
>> Message-ID: <20090623201052.173972rauz731tkw at webmail.ualberta.ca>
>> Content-Type: text/plain;       charset=ISO-8859-1;     DelSp="Yes";
>>        format="flowed"
>>
>> Hi
>>
>> Is there a way to keep all hydrogens in the ligand.pdbqt files and not
>> to merge non-polar hydrogens. My plan is to use Molecular Dynamics
>> simulations to calculate the binding energies of several
>> Receptor-Ligand complex starting from the proposed docked structures.
>> My major problem in that is: AutoDock merge the hydrogens of the
>> ligand and it's very hard to track them back to the initial
>> protonation states even with programs like open babel.
>>
>> Thanks for your time and your help is so much appreciated
>>
>> With my best regards
>> Khaled
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: 24 Jun 2009 04:54:09 -0000
>> From: "rachit raj" <rachit16raj at rediffmail.com>
>> Subject: ADL: for registration
>> To: <autodock at scripps.edu>
>> Message-ID: <20090624045409.60392.qmail at f6mail-144-154.rediffmail.com>
>> Content-Type: text/plain; charset="ISO-8859-1"
>>
>> sir
>> please include me in the daily mailing list related to autodock
>>  thanking u
>> warm regards
>> rachit raj
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Wed, 24 Jun 2009 12:29:32 +0530
>> From: Bagdevi <bagdevi.mishra at gmail.com>
>> Subject: Re: ADL: Ligands and Hydrogens
>> To: autodock at scripps.edu
>> Message-ID:
>>        <c1a055830906232359v6e0532c8l361dddba61e0a326 at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Use the "prepare_ligand4.py" script with following options.
>>
>> prepare_ligand4.py -l <ligand_file> -U lps
>>
>> This will not remove your non polar hydrogens, it will merge charges
>> and will remove lone pairs, if you want to keep your original charges
>> and lone pairs as well, you can run the script as follows
>>
>> prepare_ligand4.py -l <ligand_file> -U ' '
>>
>> Regards,
>> Bagdevi Mishra.
>>
>>
>>
>>
>> On Wed, Jun 24, 2009 at 7:40 AM, <kbarakat at ualberta.ca> wrote:
>>
>>> Hi
>>>
>>> Is there a way to keep all hydrogens in the ligand.pdbqt files and not
>>> to merge non-polar hydrogens. My plan is to use Molecular Dynamics
>>> simulations to calculate the binding energies of several
>>> Receptor-Ligand complex starting from the proposed docked structures.
>>> My major problem in that is: AutoDock merge the hydrogens of the
>>> ligand and it's very hard to track them back to the initial
>>> protonation states even with programs like open babel.
>>>
>>> Thanks for your time and your help is so much appreciated
>>>
>>> With my best regards
>>> Khaled
>>> ________________________________________________
>>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>>
>>>
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Wed, 24 Jun 2009 18:26:03 +0200
>> From: Alessandro Contini <alessandro.contini at unimi.it>
>> Subject: ADL: maximum number of map
>> To: autodock at scripps.edu
>> Message-ID: <1245860763.27808.17.camel at heisenberg>
>> Content-Type: text/plain
>>
>> Dear Autodockers,
>> I was wondering if anyone knows which is the source file of autogrid4 to
>> be modified in order to increase the maximum number of allowed maps
>> (i.e. the maximum number of ligand atom types). I did it with autogrid3
>> by setting the MAX_MAPS keywords in autocomm.h, but I don't find the
>> corresponding file for autogrid4.
>>
>> Thank you and best regards
>>
>> Alessandro Contini
>>
>>
>>
>>
>>
>>
>> ------------------------------
>>
>> ________________________________________________
>> --- ADL: AutoDock List  ---
>> http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>>
>> End of autodock Digest, Vol 58, Issue 29
>> ****************************************
>>
>>
>>
>
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