ADL: Ligands and Hydrogens (Khaled)

kbarakat at ualberta.ca kbarakat at ualberta.ca
Wed Jun 24 22:39:22 PDT 2009


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



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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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