ADL: autodock Digest, Vol 56, Issue 29

jose correa corrjose at gmail.com
Thu Apr 16 05:21:15 PDT 2009


Dear Algel Perez
Have you try with window enviroment in linux, it is very easy, only you need
to type on the ADT executable, and it runs automatically. Lo puedes ejecutar
en el ambiente gráfico, guarda la carpeta (versión linux) que bajes,
http://mgltools.scripps.edu/downloads la descomprimes y la pones en
/usr/local/bin y desde ahí lo puedes ejecutar manualmente. Te recomiendo un
curso básico de linux o pudes bajar manuales del internet (
http://www.ice.udl.es/udv/manuals/linux.pdf) dado que se requiere para
moverte sin tanto problema en el modo texto
Saludos
Espero de ayude
José Correa-Basurto
Escuela Superior de Medicina del IPN, México

2009/4/16 <autodock-request at scripps.edu>

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> Today's Topics:
>
>   1.  fail to select a model pdb file (dongming at udel.edu)
>   2.  Problem to install ADT (FRANCISCO ANGEL PEREZ LARA)
>   3.  Problem to install ADT (FRANCISCO ANGEL PEREZ LARA)
>   4.  ADT problem (FRANCISCO ANGEL PEREZ LARA)
>   5. Re:  Problem to install ADT (Sargis Dallakyan)
>   6. Re:  error in constants.h (sarah karma)
>   7.  Theory in Vina tutorial video? (mcmartin at student.matnat.uio.no)
>   8. Re:  Theory in Vina tutorial video?
>      (mswingle at jaguar1.usouthal.edu)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 15 Apr 2009 15:20:20 -0400 (EDT)
> From: <dongming at udel.edu>
> Subject: ADL: fail to select a model pdb file
> To: autodock at scripps.edu
> Message-ID: <20090415152020.DTP08118 at ms2.nss.udel.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Hi,
> I met a problem when using the autodock to docking my ligand. I cannot
> select the macromolecule which is the pdb file of my model from Modeller.
> And I realized that the pdb file from protein data bank and modeller is
> different. I guess that could be the problem of failing load the file. So
> did anyone here meet the same problem before or anyone know how to solve
> this problem? Thanks.
> Ming
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 15 Apr 2009 23:47:34 +0200
> From: FRANCISCO ANGEL PEREZ LARA <angelpl at um.es>
> Subject: ADL: Problem to install ADT
> To: mailman-owner at scripps.edu
> Message-ID: <20090415234734.18111cdm0o0bjdh2 at webmail.atica.um.es>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
>        format="flowed"
>
> HI, my name is Angel Perez-Lara,
> I am new in this of using Linux and Autodock.
> I installed Autodock in windows, but some people told me that is
> better install it in Linux.
> But when I try it the console say to me this:
> angel at angel-laptop:~$ chmod +x MGLTools-1.5.2-Linux-x86-Install
> angel at angel-laptop:~$ ./MGLTools-1.5.2-Linux-x86-Install
> setting PYTHONHOME environment
> Run PMV from  /home/angel/MGLTools-1.5.2/MGLToolsPckgs/Pmv
> angel at angel-laptop:~$ Traceback (most recent call last):
>   File "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/Pmv/__init__.py",
> line 343, in runPmv
>     title=title, withShell= not interactive, verbose=False)
>   File
> "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/Pmv/moleculeViewer.py", line
> 300, in __init__
>     verbose=verbose, trapExceptions=trapExceptions)
>   File
> "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/ViewerFramework/VF.py", line
> 347, in __init__
>     verbose=verbose)
>   File
> "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/ViewerFramework/VFGUI.py",
> line 265, in __init__
>     cnf = {"addScenarioButton": False})
>   File "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/DejaVu/Viewer.py",
> line 587, in __init__
>     c = apply(Viewer.AddCamera, (self, master, screenName,classCamera), kw)
>   File "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/DejaVu/Viewer.py",
> line 278, in AddCamera
>     c = apply( classCamera, (master, screenName, self, len(self.cameras)),
> kw)
>   File "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/DejaVu/Camera.py",
> line 4567, in __init__
>     check, cnf), **kw)
>   File "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/DejaVu/Camera.py",
> line 1594, in __init__
>     Tkinter.Widget.__init__(self, self.frame, 'togl', cnf, kw)
>   File "/home/angel/MGLTools-1.5.2/lib/python2.5/lib-tk/Tkinter.py",
> line 1930, in __init__
>     (widgetName, self._w) + extra + self._options(cnf))
> TclError: Togl: couldn't get visual
> Please include this Traceback in your bug report. Help --> Report a
> Bug in PMV/ADT.
> Could anybody help me?
> Thanks,
> Angel P?rez-Lara.
> P.D. If you could answer to me in Spanish, it will be better for me.
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 15 Apr 2009 23:47:34 +0200
> From: FRANCISCO ANGEL PEREZ LARA <angelpl at um.es>
> Subject: ADL: Problem to install ADT
> To: mailman-owner at scripps.edu
> Message-ID: <20090415234734.18111cdm0o0bjdh2 at webmail.atica.um.es>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
>        format="flowed"
>
> HI, my name is Angel Perez-Lara,
> I am new in this of using Linux and Autodock.
> I installed Autodock in windows, but some people told me that is
> better install it in Linux.
> But when I try it the console say to me this:
> angel at angel-laptop:~$ chmod +x MGLTools-1.5.2-Linux-x86-Install
> angel at angel-laptop:~$ ./MGLTools-1.5.2-Linux-x86-Install
> setting PYTHONHOME environment
> Run PMV from  /home/angel/MGLTools-1.5.2/MGLToolsPckgs/Pmv
> angel at angel-laptop:~$ Traceback (most recent call last):
>   File "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/Pmv/__init__.py",
> line 343, in runPmv
>     title=title, withShell= not interactive, verbose=False)
>   File
> "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/Pmv/moleculeViewer.py", line
> 300, in __init__
>     verbose=verbose, trapExceptions=trapExceptions)
>   File
> "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/ViewerFramework/VF.py", line
> 347, in __init__
>     verbose=verbose)
>   File
> "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/ViewerFramework/VFGUI.py",
> line 265, in __init__
>     cnf = {"addScenarioButton": False})
>   File "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/DejaVu/Viewer.py",
> line 587, in __init__
>     c = apply(Viewer.AddCamera, (self, master, screenName,classCamera), kw)
>   File "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/DejaVu/Viewer.py",
> line 278, in AddCamera
>     c = apply( classCamera, (master, screenName, self, len(self.cameras)),
> kw)
>   File "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/DejaVu/Camera.py",
> line 4567, in __init__
>     check, cnf), **kw)
>   File "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/DejaVu/Camera.py",
> line 1594, in __init__
>     Tkinter.Widget.__init__(self, self.frame, 'togl', cnf, kw)
>   File "/home/angel/MGLTools-1.5.2/lib/python2.5/lib-tk/Tkinter.py",
> line 1930, in __init__
>     (widgetName, self._w) + extra + self._options(cnf))
> TclError: Togl: couldn't get visual
> Please include this Traceback in your bug report. Help --> Report a
> Bug in PMV/ADT.
> Could anybody help me?
> Thanks,
> Angel P?rez-Lara.
> P.D. If you could answer to me in Spanish, it will be better for me.
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 15 Apr 2009 23:51:28 +0200
> From: FRANCISCO ANGEL PEREZ LARA <angelpl at um.es>
> Subject: ADL: ADT problem
> To: autodock at scripps.edu
> Message-ID: <20090415235128.11465t1pzq3n4bmo at webmail.atica.um.es>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
>        format="flowed"
>
> HI, my name is Angel Perez-Lara,
> I am new in this of using Linux and Autodock.
> I installed Autodock in windows, but some people told me that is
> better install it in Linux.
> But when I try it the console say to me this:
> angel at angel-laptop:~$ chmod +x MGLTools-1.5.2-Linux-x86-Install
> angel at angel-laptop:~$ ./MGLTools-1.5.2-Linux-x86-Install
> setting PYTHONHOME environment
> Run PMV from  /home/angel/MGLTools-1.5.2/MGLToolsPckgs/Pmv
> angel at angel-laptop:~$ Traceback (most recent call last):
>   File "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/Pmv/__init__.py",
> line 343, in runPmv
>     title=title, withShell= not interactive, verbose=False)
>   File
> "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/Pmv/moleculeViewer.py", line
> 300, in __init__
>     verbose=verbose, trapExceptions=trapExceptions)
>   File
> "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/ViewerFramework/VF.py", line
> 347, in __init__
>     verbose=verbose)
>   File
> "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/ViewerFramework/VFGUI.py",
> line 265, in __init__
>     cnf = {"addScenarioButton": False})
>   File "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/DejaVu/Viewer.py",
> line 587, in __init__
>     c = apply(Viewer.AddCamera, (self, master, screenName,classCamera), kw)
>   File "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/DejaVu/Viewer.py",
> line 278, in AddCamera
>     c = apply( classCamera, (master, screenName, self, len(self.cameras)),
> kw)
>   File "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/DejaVu/Camera.py",
> line 4567, in __init__
>     check, cnf), **kw)
>   File "/home/angel/MGLTools-1.5.2/MGLToolsPckgs/DejaVu/Camera.py",
> line 1594, in __init__
>     Tkinter.Widget.__init__(self, self.frame, 'togl', cnf, kw)
>   File "/home/angel/MGLTools-1.5.2/lib/python2.5/lib-tk/Tkinter.py",
> line 1930, in __init__
>     (widgetName, self._w) + extra + self._options(cnf))
> TclError: Togl: couldn't get visual
> Please include this Traceback in your bug report. Help --> Report a
> Bug in PMV/ADT.
> Could anybody help me?
> Thanks,
> Angel P?rez-Lara.
> P.D. If you could answer to me in Spanish, it will be better for me.
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 15 Apr 2009 15:35:55 -0700
> From: Sargis Dallakyan <sargis at scripps.edu>
> Subject: Re: ADL: Problem to install ADT
> To: autodock at scripps.edu
> Message-ID: <49E6614B.2080306 at scripps.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> FRANCISCO ANGEL PEREZ LARA wrote:
> > HI, my name is Angel Perez-Lara,
> > I am new in this of using Linux and Autodock.
> > I installed Autodock in windows, but some people told me that is better
> > install it in Linux.
> > But when I try it the console say to me this:
> > angel at angel-laptop:~$ chmod +x MGLTools-1.5.2-Linux-x86-Install
> > angel at angel-laptop:~$ ./MGLTools-1.5.2-Linux-x86-Install
> ...
> > TclError: Togl: couldn't get visual
> > Please include this Traceback in your bug report. Help --> Report a Bug
> > in PMV/ADT.
>
> Hi Angel P?rez-Lara,
>
> This is a graphics card driver related issue:
>
> http://n2.nabble.com/ADL:-MGLTools-TclError:-Togl:-couldn%27t-get-visual-RESOLVED-td2158474.html
>
> We are aware of it, and presently, the only available solution is to
> install graphics driver from your graphics card manufacturer:
> http://mgltools.scripps.edu/documentation/how-to/hardware-opengl
>
> Thank you for using our tools,
> 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
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 16 Apr 2009 11:35:04 +0330
> From: sarah karma <crimsonflower at gmail.com>
> Subject: Re: ADL: error in constants.h
> To: autodock at scripps.edu
> Message-ID:
>        <520ee36b0904160105k13d1b864p697f38e76050ccb at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> hello, dear. thank you for your helps. i saw an 0README file in
> c\1\usr\local\bin\source.
> it had written: To compile all executables, type "make install" from this
> directory.
> then i use cygwin bash shell. i go to the directory. after my user name it
> shows the directory as: /cygdrive/c/1/usr/local/bin/source
> then i type make install. it shows:
> $ make install
> bash: make: command not found
>
> OK, now what should i do?
>
> again thanks.
>
>              Sarah
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 16 Apr 2009 10:31:48 +0200 (CEST)
> From: mcmartin at student.matnat.uio.no
> Subject: ADL: Theory in Vina tutorial video?
> To: autodock at scripps.edu
> Message-ID: <eae6329d9b6e4984417c42a21364e2cf.squirrel at webmail.uio.no>
> Content-Type: text/plain;charset=iso-8859-1
>
> Hi all,
>
> So I'm watching the vina tutorial video and I got a little puzzled with the
> theory explanation. They say:
>
> "It is often said that the global minimum corresponds to the native
> conformation, however this is not correct, a deeper but narrower peak may
> actually be less preferable, because of entropy"
>
> Oleg says this while pointing at the conformation of lowest energy,
> which as I have understood, is the "strongest" binding energy. There are a
> couple of things in this sentence that I do not understand and I hope you
> can help me out:
>
> 1. Why does he talk about a ligand-receptor complex with a "native"
> conformation? I thought the term native conformation was strictly applied
> to
> proteins with the proper functional folding?
>
> 2. So I understand in the in silico experiment entropy is lost upon
> ligand-receptor binding,  especially since AutoDock neglects the solvent
> molecules (Unless the entropy of the desolvation state is taken into
> account
> with the AMBER force fields, which is not yet clear to me, even though I
> have read Cornell et al. 1995) So why is a _wider_ peak more preferable in
> terms of entropy? In other words, what does the width of the peak
> represent?
>
> I hope you can help me out!
>
> Marcus Martinez
>
>
>
> ------------------------------
>
> Message: 8
> Date: Thu, 16 Apr 2009 05:58:17 -0500
> From: mswingle at jaguar1.usouthal.edu
> Subject: Re: ADL: Theory in Vina tutorial video?
> To: autodock at scripps.edu
> Message-ID: <fb659da3243c.49e6c8f9 at jaguar1.usouthal.edu>
> Content-Type: text/plain; charset=us-ascii
>
> ----- Original Message -----
> From: mcmartin at student.matnat.uio.no
> Date: Thursday, April 16, 2009 3:33 am
> Subject: ADL: Theory in Vina tutorial video?
> To: autodock at scripps.edu
>
>
> > Hi all,
> >
> > So I'm watching the vina tutorial video and I got a little puzzled
> > with the theory explanation. They say:
> >
> > "It is often said that the global minimum corresponds to the native
> > conformation, however this is not correct, a deeper but narrower peak
> > may actually be less preferable, because of entropy"
> >
> > Oleg says this while pointing at the conformation of lowest energy,
> > which as I have understood, is the "strongest" binding energy. There
> > are a couple of things in this sentence that I do not understand and I
> hope
> > you can help me out:
> >
> > 1. Why does he talk about a ligand-receptor complex with a "native"
> > conformation? I thought the term native conformation was strictly
> > applied to proteins with the proper functional folding?
> >
>
> I think this is just intended to be a convenient shorthand for the "true"
> conformation that would, presumably, be observed
> in an NMR or crystal structure of the complex, if such was available.
> Native protein conformation is to biologically active
> protein structure as native ligand conformation is to the "active" ligand
> structure that's "competent" for binding.
>
> > 2. So I understand in the in silico experiment entropy is lost upon
> > ligand-receptor binding,  especially since AutoDock neglects the solvent
> > molecules (Unless the entropy of the desolvation state is taken into
> account
> > with the AMBER force fields, which is not yet clear to me, even though
> > I have read Cornell et al. 1995) So why is a _wider_ peak more
> > preferable in terms of entropy? In other words, what does the width of
> the peak
> > represent?
>
> Desolvation effects ARE modeled approximately in autodock's scoring
> function. I believe what Oleg is getting at is that, in
> addition to increasing entropy by displacing bound water, ligand binding is
> associated with a decrease in the
> conformational entropy of the ligand (and probably of the receptor as well
> in most cases). That is, the free ligand may
> readily take on many different low energy conformations whereas the range
> of bound conformations would be severely
> restricted by the requirement to maintain proper energetically favorable
> contacts with the receptor. A "narrow" peak in
> this context means one where the energy only stays low within some small
> region (in terms of the hypervolume defined by
> the ligand's state variables - translations, rotations, torsions) and then
> increases steeply with further changes in the
> ligand's state variables, thus limiting the size  of the conformational
> ensemble (in terms of hypervolume) that can fit near
> the energy minimum. A "wide" peak would have a larger low energy region
> (and possibly shallower gradients up the sides),
> which could accommodate a larger ensemble and, therefore, would be
> associated with a smaller decrease in
> conformational entropy. A smaller decrease in conformational entropy would
> mean, all other things being equal, a lower
> free energy of binding.
>
>
> Regards,
>
> Mark
>
>
> ------------------------------
>
> ________________________________________________
> --- ADL: AutoDock List  ---
> http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>
> End of autodock Digest, Vol 56, Issue 29
> ****************************************
>


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