ADL: how to avoid nonsensical dockings

David Crosby dcrosby at uci.edu
Wed Mar 12 17:16:49 PDT 2008


Hello again everyone! Thanks for all your great suggestions regarding
setting up a virtual screen using Cygwin. Sargis, I look forward to your
release!  I installed Ubuntu on my home desktop as a work around until I can
get cygwin to do it, but for some odd reason ADT doesn't want to start after
I install. Anyone had any experience with ADT acting strangely using Ubuntu
(a linux OS)?

Also,

I'm hoping anyone has some ideas on how I might be incorrectly setting up my
dockings such that dockings with energies of 10^7 Kcal (positive and
negative) are avoided? Sorry if this is a super newbie question, I really
appreciate your patience!

Thanks again!
Dave

-----Original Message-----
From: autodock-bounces at scripps.edu [mailto:autodock-bounces at scripps.edu] On
Behalf Of autodock-request at scripps.edu
Sent: Wednesday, March 12, 2008 10:57 AM
To: autodock at scripps.edu
Subject: autodock Digest, Vol 48, Issue 17

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Today's Topics:

   1.  Docking inside recptor / Screening using Cygwin on a PC
      (David Crosby)
   2. Re:  Docking inside recptor / Screening using Cygwin on a PC
      (Sargis Dallakyan)
   3. Re:  Constants.h (mswingle at jaguar1.usouthal.edu)
   4.  Analyzing Results (Raja S)
   5. Re:  ADT problems on Mac OS 10.5 and Leopard (lakshmi ganesan)
   6. Re:  "pdbcen" function (Tee Pioj)
   7. Re:  ADT problems on Mac OS 10.5 and Leopard (sargis at scripps.edu)
   8. Re:  ADT problems on Mac OS 10.5 and Leopard (lakshmi ganesan)
   9.  How to view docked complex? (Richa Batra)
  10.  increasing the grid points number (miriam sgobba)


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

Message: 1
Date: Tue, 11 Mar 2008 13:21:59 -0700
From: "David Crosby" <dcrosby at uci.edu>
Subject: ADL: Docking inside recptor / Screening using Cygwin on a PC
To: <autodock at scripps.edu>
Message-ID: <000301c883b5$90499600$33d1c880 at mobiledave>
Content-Type: text/plain;	charset="us-ascii"

Hello everyone, first I'd like to thank the developers of Autodock and ADT
for making such fabulous software freely available, it's a great model I
hope other developers follow!

 

I have two questions; the first is likely more simple to answer than the
latter:

 

1)       I've noticed often when I attempt to dock a ligand I'll get a
handful (perhaps 5 in 25-50) of dockings where the ligand is docked quite
literally inside the macromolecule resulting in some astronomical dG value.
Is there some setting I'm missing when I set up my grids or docking
parameters to tell Autodock to avoid nonsensical dockings?  I see you can
specify an upper energy limit under the docking parameters menu, but can I
assign a lower limit to avoid these wild results?  They throw off the
clustering data.  I'm attempting to dock a somewhat small molecule with 4-6
torsions onto a relatively small receptor (~6kd,)  I'm trying to keep my
initial dockings unbiased, so my grid envelops the entire receptor. I've
left plenty of space for the ligand to rotate freely in all configurations,
so why does my ligand often end up inside my receptor instead of on the
surface?  I understand autodock first introduce 50 randomly placed/oriented
ligands inside the grid volume and make calculations from there, but why
would it consider molecules making obviously high-energy (or low) contacts
with other atoms as preferable dockings?

 

2)       I'm curious if anyone out there is screening virtual libraries
using Windows XP and the Cygwin linux-like environment?  The tutorial at the
Autodock homepage has great instructions in a UNIX native environment, but
I'm hoping someone out there may have some helpful tips on translating that
protocol into the Cygwin environment.  I'm primarily interested in screening
the NCI's diversity set.

 

Thanks in advance!

 

David Crosby

 

Experimental Pathology

Med Surge II, Rm 311

University of California, Irvine, CA 92617

email:  <mailto:dcrosby at uci.edu> dcrosby at uci.edu

 



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

Message: 2
Date: Tue, 11 Mar 2008 15:52:13 -0800
From: Sargis Dallakyan <sargis at scripps.edu>
Subject: Re: ADL: Docking inside recptor / Screening using Cygwin on a
	PC
To: autodock at scripps.edu
Message-ID: <47D71B2D.8010106 at scripps.edu>
Content-Type: text/plain; charset=us-ascii; format=flowed

David Crosby wrote:
> 2)       I'm curious if anyone out there is screening virtual libraries
> using Windows XP and the Cygwin linux-like environment?  The tutorial at
the
> Autodock homepage has great instructions in a UNIX native environment, but
> I'm hoping someone out there may have some helpful tips on translating
that
> protocol into the Cygwin environment.  I'm primarily interested in
screening
> the NCI's diversity set.

I have been working on a tool that should enable this.
http://pyrx.sourceforge.net

PyRx is in its infancy; the first pre-alpha release will be available in a 
couple of months.

Sargis


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

Message: 3
Date: Tue, 11 Mar 2008 17:45:16 -0500
From: mswingle at jaguar1.usouthal.edu
Subject: Re: ADL: Constants.h
To: autodock at scripps.edu
Message-ID: <f5eebc3b708d.47d6c52c at jaguar1.usouthal.edu>
Content-Type: text/plain; charset=us-ascii

Hi!
As Daniel said, you can get the source code and recompile. However, you
could also simply do two separate 
jobs with 250 runs each and then use Autodock Tools to recluster. Go to the
"Analyze" menu, open both 
dlg files, then select "recluster" from the "Analyze" menu. I haven't tried
this myself but it looks like it 
should work.

Regards,

Mark

----- Original Message -----
From: Richa Batra <richa.batra at gmail.com>
Date: Tuesday, March 11, 2008 8:31 am
Subject: ADL: Constants.h
To: autodock at scripps.edu


> Hey all
> 
> i want to run 500 trials for my docking simulation.however i am unable 
> to do
> so the error that i get is "the constants.h file has maximum number of 
> runs
> stored is only 256".
> 
> I am not able to find any such file. did any one had same problem. how 
> did u
> solve it?
> please help
> 
> -- 
> Regards
> Ms Richa Batra
> Bioinformatics Centre,
> Universtiy of Pune,
> Pune, MHT, India.
> Alt. Id: batra.richa at yahoo.com
> ________________________________________________
> --- ADL: AutoDock List  ---  ---


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

Message: 4
Date: Tue, 11 Mar 2008 21:47:02 -0400
From: Raja S <rs0504 at hotmail.com>
Subject: ADL: Analyzing Results
To: <autodock at scripps.edu>
Message-ID: <BLU122-W24EC9EEB689B7F2C87141BCF080 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"


Hi all,
 
I am trying to bind a ligand to a variety of proteins, blind docking, to see
if the ligands have favorable interactions.
 
I have  a few question about the docking and analyzing the results.
 
After I run the docking, what are the best way to analyze the results? How
can I compare the results and try to prove a favorable binding?
 
Also, does it matter the x,y,z,coordinates of the ligands in doing a
docking?
 
Hope for a few responses,
 
Raja
_________________________________________________________________
Need to know the score, the latest news, or you need your Hotmail?-get your
"fix".
http://www.msnmobilefix.com/Default.aspx

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

Message: 5
Date: Wed, 12 Mar 2008 08:20:41 +0530
From: "lakshmi ganesan" <lakshmi.g85 at gmail.com>
Subject: Re: ADL: ADT problems on Mac OS 10.5 and Leopard
To: autodock at scripps.edu
Message-ID:
	<cbb32e2e0803111950h2b63e3cdqc47433e7d6ac598c at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Sargis,

Thanks a ton for pointing me to the Cjmart site. I downloaded and installed
the x11 package. By dafault it got installed in /usr/X11R6 folder. I then
renamed the X11R6 folder to X11. Then per instructions on
http://aaroniba.net/articles/x11-leopard.html, following step 3, I had to
change the "exec quartz-wm" statement in xinitrc.

Should the line be changed to: "exec /usr/X11/bin/quartz-wm".....though the
instruction says "exec /usr/X11R6/bin/quartz-wm". I do not have a X11R6
folder under /usr now.

What did you do? Do I need to anything else? Please advise.

Thanks a ton for your patience.

Lakshmi.


On 3/12/08, Sargis Dallakyan <sargis at scripps.edu> wrote:
>
> lakshmi ganesan wrote:
> > Hi Sargis,
> >
> > I followed the procedure to uninstall X11 per instructions provided on
> > http://aaroniba.net/articles/x11-leopard.html and install the tiger
> version.
> > However, the old version refused to install with the error message
> "Newer
> > Software already exists on your computer."
>
> Hi Lakshmi,
>
> I was getting exactly the same message that's why I used X11 from another
> machine that had X11 already installed.
>
> > Since this is my first mac and I do not have access to other versions of
> > X11, is it possible for you to upload the /usr/X11 files that you have
> used
> > successfully?
>
>
>
http://cjmart.in/2006/12/01/install-x11-on-tiger-without-the-tiger-install-d
vd
>
> You can access this link from our website as well:
> http://mgltools.scripps.edu/documentation/faq/x-error-on-startup-mac-os-x
>
> Good luck,
> Sargis
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>


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

Message: 6
Date: Wed, 12 Mar 2008 05:30:38 +0000 (GMT)
From: Tee Pioj <tee_piorj at yahoo.com>
Subject: Re: ADL: "pdbcen" function
To: autodock at scripps.edu
Message-ID: <447550.48503.qm at web59311.mail.re1.yahoo.com>
Content-Type: text/plain; charset=us-ascii

Hello, Antonio Cavazzuti 
Again you  should solve this problem with these command:

$cd /usr/local/bin

and then 

$ln -s /usr/local/dist305/share/pdbcen pdbcen

This commamd is a link command (ln). This put link of pdbcen command into
bin directory. Try typing pdbcen again. It gonna work.

Best luck,
Tee Piroj

----- Original Message ----
From: Antonio Cavazzuti <acavazzuti at ipb.csic.es>
To: autodock at scripps.edu
Sent: Tuesday, March 11, 2008 10:21:16 PM
Subject: ADL: "pdbcen" function

Hi,
I am using Autodock4 Autogrid4 and ADT 1.5 under Ubuntu. I had problems with
grid setting up. Tee Piroj (thanks you!!) previously suggested me to use
"pdbcen" command to obtain center of binding site and put them in grid
dialogue box. 
Finally I had to manually calculate center of binding site because "pdbcen"
doesn't work.. I open a terminal windows, I change directory where my pdb
file
is and I enter

pdbcen myfile.pdb

...but the answer is "command not found"

How can I solve this? 
Thanks in advance,
Antonio



Instituto de Parasitologia y Biomedicina "Lopez-Neyra"
Avda. Conocimiento S/N
Parque Tecnologico Ciencias de la Salud
18100 Armilla - GRANADA
Spain
Tlf: 958181621
Fax: 958181632
http://www.ipb.csic.es
--

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---


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

Message: 7
Date: Tue, 11 Mar 2008 22:34:59 -0700 (PDT)
From: sargis at scripps.edu
Subject: Re: ADL: ADT problems on Mac OS 10.5 and Leopard
To: autodock at scripps.edu
Message-ID:
	<3476.71.138.63.235.1205300099.squirrel at webmail.scripps.edu>
Content-Type: text/plain;charset=iso-8859-1

> Hi Sargis,
>
> Thanks a ton for pointing me to the Cjmart site. I downloaded and
> installed
> the x11 package. By dafault it got installed in /usr/X11R6 folder. I then
> renamed the X11R6 folder to X11. Then per instructions on
> http://aaroniba.net/articles/x11-leopard.html, following step 3, I had to
> change the "exec quartz-wm" statement in xinitrc.
>
> Should the line be changed to: "exec /usr/X11/bin/quartz-wm".....though
> the
> instruction says "exec /usr/X11R6/bin/quartz-wm". I do not have a X11R6
> folder under /usr now.
>
> What did you do? Do I need to anything else? Please advise.

Hi Lakshmi,

I did change xinitrc, however you can make a link or hard copy of /usr/X11
as /usr/X11R6 so that either way it works. Just make sure that you can
start X11.app.

Sargis



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

Message: 8
Date: Wed, 12 Mar 2008 11:18:49 +0530
From: "lakshmi ganesan" <lakshmi.g85 at gmail.com>
Subject: Re: ADL: ADT problems on Mac OS 10.5 and Leopard
To: autodock at scripps.edu
Message-ID:
	<cbb32e2e0803112248x6c0c170dhd53cd836717737cc at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Thank you, Sargis. Will try that. So you changed the line in xinitrc
to  "exec /usr/X11/bin/quartz-wm", right?

Will keep you posted.

Regards, Lakshmi


On 3/12/08, sargis at scripps.edu <sargis at scripps.edu> wrote:
>
> > Hi Sargis,
> >
> > Thanks a ton for pointing me to the Cjmart site. I downloaded and
> > installed
> > the x11 package. By dafault it got installed in /usr/X11R6 folder. I
> then
> > renamed the X11R6 folder to X11. Then per instructions on
> > http://aaroniba.net/articles/x11-leopard.html, following step 3, I had
> to
> > change the "exec quartz-wm" statement in xinitrc.
> >
> > Should the line be changed to: "exec /usr/X11/bin/quartz-wm".....though
> > the
> > instruction says "exec /usr/X11R6/bin/quartz-wm". I do not have a X11R6
> > folder under /usr now.
> >
> > What did you do? Do I need to anything else? Please advise.
>
> Hi Lakshmi,
>
> I did change xinitrc, however you can make a link or hard copy of /usr/X11
> as /usr/X11R6 so that either way it works. Just make sure that you can
> start X11.app.
>
> Sargis
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>


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

Message: 9
Date: Wed, 12 Mar 2008 14:35:52 +0530
From: "Richa Batra" <richa.batra at gmail.com>
Subject: ADL: How to view docked complex?
To: autodock at scripps.edu
Message-ID:
	<b999f90c0803120205n6d9461deyf33cbb87e1834959 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Dear All
I have got some dlg files. n there are some 100 trials for each of them so i
have 100 docked conformations.
can anyone please tell me how to visualize these docked conformations.

Regards
Ms Richa Batra
Bioinformatics Centre,
Universtiy of Pune,
Pune, MHT, India.
Alt. Id: batra.richa at yahoo.com


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

Message: 10
Date: Wed, 12 Mar 2008 18:56:48 +0100
From: "miriam sgobba" <miriam.sgobba at gmail.com>
Subject: ADL: increasing the grid points number
To: autodock at scripps.edu
Message-ID:
	<4ea94de60803121056j6d481e77x6d5f89e1a744c8d6 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi all,
I would like to built a grid with a number of points higher than 126 x 126 x
126 and a spacing of 0.375 using AutoDock4. To this end, I read that I must
modify the number in the MAX_GRIDS_PTS line of the autocomm.h file (in the
src/autodock/ directory) and then I re-compile autogrid. Is this a right
operation?
What does this operation implies?
Can this operation cause problems of swapping or memory?
Does anyone use a grid with these parameters?

Appreciate any help.

Thank you very much in advance.
Miriam


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

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