ADL: AutoDock Vina new beta release

[arthur olson]

Dear AutoDock Users,

I want to alert AutoDock users to a new beta version of Vina, which is
now called AutoDock Vina, a new docking code developed by Oleg Trott in
my lab.  AutoDock Vena uses the same format for the ligand and receptor
files as AutoDock4, which can be prepared by AutoDock Tools, however its
input is much simpler, and there is no need to run AutoGrid before
runing the docking.  The scoring and optimization procedures in AutoDock
Vina are quite different than those in AutoDock4.

A paper announcing and describing AutoDock Vina is about to be submitted
for publicataion.  In the paper we compare its performance relative to
AutoDock4.  We have found AutoDock Vina is considerably faster than
AutoDock4, with comparable or better  docked structures for many complexes.

The newly released AutoDock Vina 1.0 beta 03 has the following changes
from the previous release:

(1) Improved estimation of the statistical influence of the
flexibility of the ligand on its free energy of binding
(2) Optimization of multiple interacting ligands is disabled
 If you run Vina now with 0 or 2 or more ligands, you'll get an error, saying
that this version requires exactly one ligand.

If people have a particular need to dock multiple ligands simultaneously, please let us know and we can discuss future possibilities.

AutoDock Vina 1.0 beta 03 is distributed as binary executables for both Linux and Windows platforms (sorry, no Mac OSX version yet).  It can be downloaded from vina.scripps.edu or via links from autodock.scripps.edu.  I encourage you to try the beta version and provide feedback to us.

Thanks,

Art Olson


--
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@

Arthur J. Olson, Ph.D.
Professor
Department of Molecular Biology
The Scripps Research Institute
La Jolla, CA 92037
tel. [phone]
fax. [phone]
http://www.scripps.edu/pub/olson-web

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

[Douglas Houston]

Dear Dr. Olson,

Your lab's docking program sounds very interesting. Since I can't see  
the paper yet, do you have any theories about why your program appears  
to produce superior dockings despite running more quickly?

I presume that using ADT means you merge non-polar hydrogens? Could  
you also tell me how you add hydrogens and assign partial charges to  
your receptor molecule?

I'll definitely give your beta a whirl and see how it goes,

cheers,

Doug


Quoting arthur olson <[hidden email]>:

> Dear AutoDock Users,
>
> I want to alert AutoDock users to a new beta version of Vina, which is
> now called AutoDock Vina, a new docking code developed by Oleg Trott in
> my lab.  AutoDock Vena uses the same format for the ligand and receptor
> files as AutoDock4, which can be prepared by AutoDock Tools, however
> its input is much simpler, and there is no need to run AutoGrid before
> runing the docking.  The scoring and optimization procedures in
> AutoDock Vina are quite different than those in AutoDock4.
>
> A paper announcing and describing AutoDock Vina is about to be
> submitted for publicataion.  In the paper we compare its performance
> relative to AutoDock4.  We have found AutoDock Vina is considerably
> faster than AutoDock4, with comparable or better  docked structures for
> many complexes.
>
> The newly released AutoDock Vina 1.0 beta 03 has the following changes
> from the previous release:
>
> (1) Improved estimation of the statistical influence of the
> flexibility of the ligand on its free energy of binding
> (2) Optimization of multiple interacting ligands is disabled
> If you run Vina now with 0 or 2 or more ligands, you'll get an error, saying
> that this version requires exactly one ligand.
>
> If people have a particular need to dock multiple ligands
> simultaneously, please let us know and we can discuss future
> possibilities.
>
> AutoDock Vina 1.0 beta 03 is distributed as binary executables for both
> Linux and Windows platforms (sorry, no Mac OSX version yet).  It can be
> downloaded from vina.scripps.edu or via links from
> autodock.scripps.edu.  I encourage you to try the beta version and
> provide feedback to us.
>
> Thanks,
>
> Art Olson
>
>
> --
> @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
>
> Arthur J. Olson, Ph.D.
> Professor
> Department of Molecular Biology
> The Scripps Research Institute
> La Jolla, CA 92037
> tel. [phone] fax. [phone]
> http://www.scripps.edu/pub/olson-web
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

_____________________________________________
Dr. Douglas R. Houston
Room 3.23
Institute of Structural and Molecular Biology
Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. [phone]

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



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

[arthur olson]

Dear Doug,

AutoDock Vina uses a simpler scoring function than AutoDock.  It does
not use atomic charges but rather only atom types, using a different
atom typing scheme internally. The scoring function is based on a
machine learning approach trained against both conformation and
affinity.  The gains in performance are, in large part, due to the use
of the gradient in the optimization method that gives it a "sense of
direction" from a single evaluation.

Currently, our theory regarding its improved docking results speaks to
the possibly too strong assumptions that are made in  the physics-based
scoring methods, and to the fact that our scoring approach uses both
experimental structure and affinity in optimizing the form and weights
of the scoring terms.

Let us know how it works for you.

Best regards,

Art Olson



Douglas Houston wrote:

> Dear Dr. Olson,
>
> Your lab's docking program sounds very interesting. Since I can't see
> the paper yet, do you have any theories about why your program appears
> to produce superior dockings despite running more quickly?
>
> I presume that using ADT means you merge non-polar hydrogens? Could
> you also tell me how you add hydrogens and assign partial charges to
> your receptor molecule?
>
> I'll definitely give your beta a whirl and see how it goes,
>
> cheers,
>
> Doug
>
>
> Quoting arthur olson <[hidden email]>:
>
>> Dear AutoDock Users,
>>
>> I want to alert AutoDock users to a new beta version of Vina, which is
>> now called AutoDock Vina, a new docking code developed by Oleg Trott in
>> my lab.  AutoDock Vena uses the same format for the ligand and receptor
>> files as AutoDock4, which can be prepared by AutoDock Tools, however
>> its input is much simpler, and there is no need to run AutoGrid before
>> runing the docking.  The scoring and optimization procedures in
>> AutoDock Vina are quite different than those in AutoDock4.
>>
>> A paper announcing and describing AutoDock Vina is about to be
>> submitted for publicataion.  In the paper we compare its performance
>> relative to AutoDock4.  We have found AutoDock Vina is considerably
>> faster than AutoDock4, with comparable or better  docked structures for
>> many complexes.
>>
>> The newly released AutoDock Vina 1.0 beta 03 has the following changes
>> from the previous release:
>>
>> (1) Improved estimation of the statistical influence of the
>> flexibility of the ligand on its free energy of binding
>> (2) Optimization of multiple interacting ligands is disabled
>> If you run Vina now with 0 or 2 or more ligands, you'll get an error,
>> saying
>> that this version requires exactly one ligand.
>>
>> If people have a particular need to dock multiple ligands
>> simultaneously, please let us know and we can discuss future
>> possibilities.
>>
>> AutoDock Vina 1.0 beta 03 is distributed as binary executables for both
>> Linux and Windows platforms (sorry, no Mac OSX version yet).  It can be
>> downloaded from vina.scripps.edu or via links from
>> autodock.scripps.edu.  I encourage you to try the beta version and
>> provide feedback to us.
>>
>> Thanks,
>>
>> Art Olson
>>
>>
>> --
>> @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
>>
>> Arthur J. Olson, Ph.D.
>> Professor
>> Department of Molecular Biology
>> The Scripps Research Institute
>> La Jolla, CA 92037
>> tel. [phone] fax. [phone]
>> http://www.scripps.edu/pub/olson-web
>>
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>
>
>
> _____________________________________________
> Dr. Douglas R. Houston
> Room 3.23
> Institute of Structural and Molecular Biology
> Michael Swann Building
> King's Buildings
> University of Edinburgh
> Edinburgh, EH9 3JR, UK
> Tel. [phone]
>

--
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@

Arthur J. Olson, Ph.D.
Professor
Department of Molecular Biology
The Scripps Research Institute
La Jolla, CA 92037
tel. [phone]
fax. [phone]
http://www.scripps.edu/pub/olson-web

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

[Stephen P. Molnar]

I have run the tutorial on both my 64 bit single core Linux machine and
my MS Vista 64 bit dual core laptop.

The results are very nice.  Certainly the execution is faster than
autodock.  I would like to see details of the algorithm.

I think it would be helpful if the tutorial were downloadable

--
Stephen P. Molnar, Ph.D. Life is a fuzzy set
Foundation for Chemistry Stochastic and multivariate
http://www.geocities.com/FoundationForChemistry



arthur olson wrote:

> Dear AutoDock Users,
>
> I want to alert AutoDock users to a new beta version of Vina, which is
> now called AutoDock Vina, a new docking code developed by Oleg Trott
> in my lab.  AutoDock Vena uses the same format for the ligand and
> receptor files as AutoDock4, which can be prepared by AutoDock Tools,
> however its input is much simpler, and there is no need to run
> AutoGrid before runing the docking.  The scoring and optimization
> procedures in AutoDock Vina are quite different than those in AutoDock4.
>
> A paper announcing and describing AutoDock Vina is about to be
> submitted for publicataion.  In the paper we compare its performance
> relative to AutoDock4.  We have found AutoDock Vina is considerably
> faster than AutoDock4, with comparable or better  docked structures
> for many complexes.
>
> The newly released AutoDock Vina 1.0 beta 03 has the following changes
> from the previous release:
>
> (1) Improved estimation of the statistical influence of the
> flexibility of the ligand on its free energy of binding
> (2) Optimization of multiple interacting ligands is disabled
> If you run Vina now with 0 or 2 or more ligands, you'll get an error,
> saying
> that this version requires exactly one ligand.
>
> If people have a particular need to dock multiple ligands
> simultaneously, please let us know and we can discuss future
> possibilities.
>
> AutoDock Vina 1.0 beta 03 is distributed as binary executables for
> both Linux and Windows platforms (sorry, no Mac OSX version yet).  It
> can be downloaded from vina.scripps.edu or via links from
> autodock.scripps.edu.  I encourage you to try the beta version and
> provide feedback to us.
>
> Thanks,
>
> Art Olson
>
>

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

[George Tzotzos]

Any plans for Mac OSX?

All the best

George

On Feb 19, 2009, at 9:11 PM, arthur olson wrote:

> Dear AutoDock Users,
>
> I want to alert AutoDock users to a new beta version of Vina, which  
> is now called AutoDock Vina, a new docking code developed by Oleg  
> Trott in my lab.  AutoDock Vena uses the same format for the ligand  
> and receptor files as AutoDock4, which can be prepared by AutoDock  
> Tools, however its input is much simpler, and there is no need to  
> run AutoGrid before runing the docking.  The scoring and  
> optimization procedures in AutoDock Vina are quite different than  
> those in AutoDock4.
>
> A paper announcing and describing AutoDock Vina is about to be  
> submitted for publicataion.  In the paper we compare its performance  
> relative to AutoDock4.  We have found AutoDock Vina is considerably  
> faster than AutoDock4, with comparable or better  docked structures  
> for many complexes.
>
> The newly released AutoDock Vina 1.0 beta 03 has the following  
> changes from the previous release:
>
> (1) Improved estimation of the statistical influence of the
> flexibility of the ligand on its free energy of binding
> (2) Optimization of multiple interacting ligands is disabled
> If you run Vina now with 0 or 2 or more ligands, you'll get an  
> error, saying
> that this version requires exactly one ligand.
>
> If people have a particular need to dock multiple ligands  
> simultaneously, please let us know and we can discuss future  
> possibilities.
>
> AutoDock Vina 1.0 beta 03 is distributed as binary executables for  
> both Linux and Windows platforms (sorry, no Mac OSX version yet).  
> It can be downloaded from vina.scripps.edu or via links from  
> autodock.scripps.edu.  I encourage you to try the beta version and  
> provide feedback to us.
>
> Thanks,
>
> Art Olson
>
>
> --
> @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
>
> Arthur J. Olson, Ph.D.
> Professor
> Department of Molecular Biology
> The Scripps Research Institute
> La Jolla, CA 92037
> tel. [phone] fax. [phone]
> http://www.scripps.edu/pub/olson-web
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list 
> ---

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

[Ajaya Shrestha]

Dear Dr. Olson,

I have downloaded autodock vina recently and I am trying to conduct the docking of the ligand into the protein molecule of the tutorial. I am using Autodock 4.0 and I have found that the no. of torsion of the ligand is different than that in the tutorial. In the tutorial no. of rotable bonds were 6 and after making a bond rotable the total no. became 7. But in my case, the no. of rotable bonds are 5. The bond between pyridine and pyrimidine moiety is non-rotable in my case. Could you please suggest me the reason for this problem.

Otherwise, the program seems to be faster than the regular Autodock program.
Hope to have your kind suggestion soon.

Ajaya Shrestha

_________________________________________________________________
Show them the way! Add maps and directions to your party invites.
http://www.microsoft.com/windows/windowslive/products/events.aspx
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

[Oleg Trott]

Ajaya,

I believe what you are seeing happens before Vina is even launched, so
this can't be a problem in AutoDock Vina. AutoDock 4.x is not used in
the tutorial at all.

What version of MGLTools/ADT are you using? With this information, its
authors or maintainers may be able to help you further.

Oleg

On Sun, Feb 22, 2009 at 11:41 PM, Ajaya Shrestha <[hidden email]> wrote:

>
>
> Dear Dr. Olson,
>
> I have downloaded autodock vina recently and I am trying to conduct the docking of the ligand into the protein molecule of the tutorial. I am using Autodock 4.0 and I have found that the no. of torsion of the ligand is different than that in the tutorial. In the tutorial no. of rotable bonds were 6 and after making a bond rotable the total no. became 7. But in my case, the no. of rotable bonds are 5. The bond between pyridine and pyrimidine moiety is non-rotable in my case. Could you please suggest me the reason for this problem.
>
> Otherwise, the program seems to be faster than the regular Autodock program.
> Hope to have your kind suggestion soon.
>
> Ajaya Shrestha
>
> _________________________________________________________________
> Show them the way! Add maps and directions to your party invites.
> http://www.microsoft.com/windows/windowslive/products/events.aspx
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>

--
Oleg Trott, Ph.D. (Columbia University)

http://olegtrott.com

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

[Oleg Trott]

Stephen,

I added a link to download the tutorial as wmv. Thanks for the
suggestion and confirming it works on Microsoft Vista, as expected.
We'll send an announcement when the paper describing the details of
Vina's operation is published, but some of them are talked about on
the "Features" and "Manual" web pages.

Oleg

On Sat, Feb 21, 2009 at 7:27 AM, Stephen P. Molnar
<[hidden email]> wrote:

> I have run the tutorial on both my 64 bit single core Linux machine and my
> MS Vista 64 bit dual core laptop.
>
> The results are very nice.  Certainly the execution is faster than autodock.
>  I would like to see details of the algorithm.
>
> I think it would be helpful if the tutorial were downloadable
>
> --
> Stephen P. Molnar, Ph.D.                Life is a fuzzy set
> Foundation for Chemistry                Stochastic and multivariate
> http://www.geocities.com/FoundationForChemistry
>
>
>
> arthur olson wrote:
>>
>> Dear AutoDock Users,
>>
>> I want to alert AutoDock users to a new beta version of Vina, which is now
>> called AutoDock Vina, a new docking code developed by Oleg Trott in my lab.
>>  AutoDock Vena uses the same format for the ligand and receptor files as
>> AutoDock4, which can be prepared by AutoDock Tools, however its input is
>> much simpler, and there is no need to run AutoGrid before runing the
>> docking.  The scoring and optimization procedures in AutoDock Vina are quite
>> different than those in AutoDock4.
>>
>> A paper announcing and describing AutoDock Vina is about to be submitted
>> for publicataion.  In the paper we compare its performance relative to
>> AutoDock4.  We have found AutoDock Vina is considerably faster than
>> AutoDock4, with comparable or better  docked structures for many complexes.
>>
>> The newly released AutoDock Vina 1.0 beta 03 has the following changes
>> from the previous release:
>>
>> (1) Improved estimation of the statistical influence of the
>> flexibility of the ligand on its free energy of binding
>> (2) Optimization of multiple interacting ligands is disabled
>> If you run Vina now with 0 or 2 or more ligands, you'll get an error,
>> saying
>> that this version requires exactly one ligand.
>>
>> If people have a particular need to dock multiple ligands simultaneously,
>> please let us know and we can discuss future possibilities.
>>
>> AutoDock Vina 1.0 beta 03 is distributed as binary executables for both
>> Linux and Windows platforms (sorry, no Mac OSX version yet).  It can be
>> downloaded from vina.scripps.edu or via links from autodock.scripps.edu.  I
>> encourage you to try the beta version and provide feedback to us.
>>
>> Thanks,
>>
>> Art Olson
>>
>>
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>

--
Oleg Trott, Ph.D. (Columbia University)

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

[Ajaya Shrestha]

Dear Dr. Oleg,

Thank you for your kind response.
The version of Autodock tools I am using is MGL Tools/ADT 1.5.2 and I have followed the tutorial as it is, but I have got different result than that in tutorial. The energy value was higher than the tutorial. I think the problem is due to the number of rotable bonds of the ligand. So, could you please help me to sought out this problem.

Looking forward to get your kind suggestions.

Ajaya

> Date: Mon, 23 Feb 2009 12:21:30 -0800
> From: [hidden email]
> To: [hidden email]
> Subject: Re: ADL: problem with ligand in autodock vina
>
> Ajaya,
>
> I believe what you are seeing happens before Vina is even launched, so
> this can't be a problem in AutoDock Vina. AutoDock 4.x is not used in
> the tutorial at all.
>
> What version of MGLTools/ADT are you using? With this information, its
> authors or maintainers may be able to help you further.
>
> Oleg
>
> On Sun, Feb 22, 2009 at 11:41 PM, Ajaya Shrestha <[hidden email]> wrote:
> >
> >
> > Dear Dr. Olson,
> >
> > I have downloaded autodock vina recently and I am trying to conduct the docking of the ligand into the protein molecule of the tutorial. I am using Autodock 4.0 and I have found that the no. of torsion of the ligand is different than that in the tutorial. In the tutorial no. of rotable bonds were 6 and after making a bond rotable the total no. became 7. But in my case, the no. of rotable bonds are 5. The bond between pyridine and pyrimidine moiety is non-rotable in my case. Could you please suggest me the reason for this problem.
> >
> > Otherwise, the program seems to be faster than the regular Autodock program.
> > Hope to have your kind suggestion soon.
> >
> > Ajaya Shrestha
> >
> > _________________________________________________________________
> > Show them the way! Add maps and directions to your party invites.
> > http://www.microsoft.com/windows/windowslive/products/events.aspx
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
>
>
>
> --
> Oleg Trott, Ph.D. (Columbia University)
>
> http://olegtrott.com
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

_________________________________________________________________
More than messages–check out the rest of the Windows Live™.
http://www.microsoft.com/windows/windowslive/
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

[Ruth Huey]

Hi Ajaya,

The problem you encountered is caused by a bug in MGLTools version 1.5.2.
An update for MGLTools version 1.5.2 to fix this problem is available.

Here are the steps to obtain and install the update via ADT:

1. Click on the "Help" menu in the top right corner of the ADT GUI.

2. Choose "Update" in the dropdown menu

3. In the "Update MGLTools" widget which opens:
         click "Check for Updates"

4. The following message is displayed along with buttons "Install" and
"Save to File":

    Available updates:
    Updates - Tested Builds
    2008/11/19 "Install"  "Save to File"  

5. Click on the "Install" button
 
6. You will the see this message with "OK" and "Cancel" buttons:
 "You will need to restart AutoDockTools for the changes to take place.
Would you like to restart AutoDockTools now?
   "OK"   "Cancel"

7. Click on the "OK"  button

This updates your local installation of MGLTools.

The updated version should properly classify the rotatable bond between
the two cycles.
Please let me know if it doesn't or if you encounter other problems.

Thank you for your interest in our tools and for your patience!

                Ruth


Ajaya Shrestha wrote:

>
> I have downloaded autodock vina recently and I am trying to conduct the docking of the ligand into the protein molecule of the tutorial. I am using Autodock 4.0 and I have found that the no. of torsion of the ligand is different than that in the tutorial. In the tutorial no. of rotable bonds were 6 and after making a bond rotable the total no. became 7. But in my case, the no. of rotable bonds are 5. The bond between pyridine and pyrimidine moiety is non-rotable in my case. Could you please suggest me the reason for this problem.
>
> Otherwise, the program seems to be faster than the regular Autodock program.
> Hope to have your kind suggestion soon.
>
> Ajaya Shrestha
>
> _________________________________________________________________
> Show them the way! Add maps and directions to your party invites.
> http://www.microsoft.com/windows/windowslive/products/events.aspx
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>  

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

[Ajaya Shrestha]

Dear Dr. Ruth,

Thank you very much for your kind suggestion.
I have solved the problem, now I can see appropriate rotable bonds in ADT.

Sincerely,
Ajaya

> Date: Tue, 24 Feb 2009 09:28:46 -0800
> From: [hidden email]
> To: [hidden email]
> Subject: Re: ADL: problem with ligand in autodock vina
>
> Hi Ajaya,
>
> The problem you encountered is caused by a bug in MGLTools version 1.5.2.
> An update for MGLTools version 1.5.2 to fix this problem is available.
>
> Here are the steps to obtain and install the update via ADT:
>
> 1. Click on the "Help" menu in the top right corner of the ADT GUI.
>
> 2. Choose "Update" in the dropdown menu
>
> 3. In the "Update MGLTools" widget which opens:
>          click "Check for Updates"
>
> 4. The following message is displayed along with buttons "Install" and
> "Save to File":
>
>     Available updates:
>     Updates - Tested Builds
>     2008/11/19 "Install"  "Save to File"  
>
> 5. Click on the "Install" button
>  
> 6. You will the see this message with "OK" and "Cancel" buttons:
>  "You will need to restart AutoDockTools for the changes to take place.
> Would you like to restart AutoDockTools now?
>    "OK"   "Cancel"
>
> 7. Click on the "OK"  button
>
> This updates your local installation of MGLTools.
>
> The updated version should properly classify the rotatable bond between
> the two cycles.
> Please let me know if it doesn't or if you encounter other problems.
>
> Thank you for your interest in our tools and for your patience!
>
>                 Ruth
>
>
> Ajaya Shrestha wrote:
> >
> > I have downloaded autodock vina recently and I am trying to conduct the docking of the ligand into the protein molecule of the tutorial. I am using Autodock 4.0 and I have found that the no. of torsion of the ligand is different than that in the tutorial. In the tutorial no. of rotable bonds were 6 and after making a bond rotable the total no. became 7. But in my case, the no. of rotable bonds are 5. The bond between pyridine and pyrimidine moiety is non-rotable in my case. Could you please suggest me the reason for this problem.
> >
> > Otherwise, the program seems to be faster than the regular Autodock program.
> > Hope to have your kind suggestion soon.
> >
> > Ajaya Shrestha
> >
> > _________________________________________________________________
> > Show them the way! Add maps and directions to your party invites.
> > http://www.microsoft.com/windows/windowslive/products/events.aspx
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >  
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

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[hanthuy]

I'm using both AutoDock4 and AutoDock Vina.
I used tourial of AutoDock4 in AutoDock Vina and realized that it take more time than AutoDock4.
And I wonder that which algorithm used in AutoDock Vina (LA,GA,LGA...)?
Thanks.

[xsyourpal]

Dr. Olson,

Are you planning to release the Autodock Vina source code at some point to allow a detailed analysis and comparison with the Autodock4 ?  

Thanks

hanthuy wrote:

I'm using both AutoDock4 and AutoDock Vina.
I used tourial of AutoDock4 in AutoDock Vina and realized that it take more time than AutoDock4.
And I wonder that which algorithm used in AutoDock Vina (LA,GA,LGA...)?
Thanks.

[hanthuy]

I just want to know clearly about this version. Because there are some algorithms, and each of them just suit for some of case. Do you mean that AD vina just use one type of algorithm for search?

[xsyourpal]

Dr. Olson,

Was it not possible to simply extend the existing Autodock4 software to include the optimizations of Autodock Vina ?  one possibility would have been to add a new mode of operation and search method, many such configuration options are already supported in Autodock4.  

Does the current and future releases of Autodock Vina suggest end of road for Autodock4 ? or do you believe that Autodock Vina will also be released as GPL open source to allow for the community to work out a efficient way to continue using both.

Thanks.

[hanthuy]

So, That's all secret?
AD Vina will be a commercial version! Clear.

Thanks.
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[ishwar chandra]

Hi All Greetings
I would like to know that Autodock Vina could be run on Windows XP also or
on Vista only . We also need to install ADT, Cygwin, Python on our machne.
Plaese tell. Thank You.
Regards
 Ishwar

On 2/26/09, hanthuy <[hidden email]> wrote:

>
>
> I just want to know clearly about this version. Because there are some
> algorithms, and each of them just suit for some of case. Do you mean that
> AD
> vina just use one type of algorithm for search?
>
>
> --
> View this message in context:
> http://n2.nabble.com/ADL%3A-AutoDock-Vina-new-beta-release-tp2355177p2390405.html
>
> Sent from the AutoDock mailing list archive at Nabble.com.
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>

________________________________________________
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[bagdevi]

Dr. Art Olson and Dr. Oleg Trott,

I tested the vina on Linux platform and compared the results with the
autodock4. The vina is really better than the flexible docking with
autodock4. Its "easy to use" feature is simply great. But can you please
make it clear that, weather you would be releasing its source code in future
or planning to commercialise it, as some user in this mailing list wrote
earlier.


Regards,
Bagdevi Mishra.



On Tue, Feb 24, 2009 at 2:40 AM, Oleg Trott <[hidden email]> wrote:

> Stephen,
>
> I added a link to download the tutorial as wmv. Thanks for the
> suggestion and confirming it works on Microsoft Vista, as expected.
> We'll send an announcement when the paper describing the details of
> Vina's operation is published, but some of them are talked about on
> the "Features" and "Manual" web pages.
>
> Oleg
>
> On Sat, Feb 21, 2009 at 7:27 AM, Stephen P. Molnar
> <[hidden email]> wrote:
> > I have run the tutorial on both my 64 bit single core Linux machine and
> my
> > MS Vista 64 bit dual core laptop.
> >
> > The results are very nice.  Certainly the execution is faster than
> autodock.
> >  I would like to see details of the algorithm.
> >
> > I think it would be helpful if the tutorial were downloadable
> >
> > --
> > Stephen P. Molnar, Ph.D.                Life is a fuzzy set
> > Foundation for Chemistry                Stochastic and multivariate
> > http://www.geocities.com/FoundationForChemistry
> >
> >
> >
> > arthur olson wrote:
> >>
> >> Dear AutoDock Users,
> >>
> >> I want to alert AutoDock users to a new beta version of Vina, which is
> now
> >> called AutoDock Vina, a new docking code developed by Oleg Trott in my
> lab.
> >>  AutoDock Vena uses the same format for the ligand and receptor files as
> >> AutoDock4, which can be prepared by AutoDock Tools, however its input is
> >> much simpler, and there is no need to run AutoGrid before runing the
> >> docking.  The scoring and optimization procedures in AutoDock Vina are
> quite
> >> different than those in AutoDock4.
> >>
> >> A paper announcing and describing AutoDock Vina is about to be submitted
> >> for publicataion.  In the paper we compare its performance relative to
> >> AutoDock4.  We have found AutoDock Vina is considerably faster than
> >> AutoDock4, with comparable or better  docked structures for many
> complexes.
> >>
> >> The newly released AutoDock Vina 1.0 beta 03 has the following changes
> >> from the previous release:
> >>
> >> (1) Improved estimation of the statistical influence of the
> >> flexibility of the ligand on its free energy of binding
> >> (2) Optimization of multiple interacting ligands is disabled
> >> If you run Vina now with 0 or 2 or more ligands, you'll get an error,
> >> saying
> >> that this version requires exactly one ligand.
> >>
> >> If people have a particular need to dock multiple ligands
> simultaneously,
> >> please let us know and we can discuss future possibilities.
> >>
> >> AutoDock Vina 1.0 beta 03 is distributed as binary executables for both
> >> Linux and Windows platforms (sorry, no Mac OSX version yet).  It can be
> >> downloaded from vina.scripps.edu or via links from autodock.scripps.edu.
>  I
> >> encourage you to try the beta version and provide feedback to us.
> >>
> >> Thanks,
> >>
> >> Art Olson
> >>
> >>
> >
> >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
>
>
>
> --
> Oleg Trott, Ph.D. (Columbia University)
>
> http://olegtrott.com
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>

________________________________________________
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[Rajan75]

Dear Olson,

First, my heartiest congrats for this excellent version, and due appreciation of Oleg's hard work.

Now, here is my problem:

When, I bind the inhibitor to the site, I see a geometry totally opposite to that predicted. For example, if the inhibitor binds exp as A-B, I see binding as B-A. The position though is conserved.

I am not sure, what mistake I am doing here. Please provide me some solution.

Thanks,

-Rajan

arthur olson wrote:

Dear AutoDock Users,

I want to alert AutoDock users to a new beta version of Vina, which is
now called AutoDock Vina, a new docking code developed by Oleg Trott in
my lab.  AutoDock Vena uses the same format for the ligand and receptor
files as AutoDock4, which can be prepared by AutoDock Tools, however its
input is much simpler, and there is no need to run AutoGrid before
runing the docking.  The scoring and optimization procedures in AutoDock
Vina are quite different than those in AutoDock4.

A paper announcing and describing AutoDock Vina is about to be submitted
for publicataion.  In the paper we compare its performance relative to
AutoDock4.  We have found AutoDock Vina is considerably faster than
AutoDock4, with comparable or better  docked structures for many complexes.

The newly released AutoDock Vina 1.0 beta 03 has the following changes
from the previous release:

(1) Improved estimation of the statistical influence of the
flexibility of the ligand on its free energy of binding
(2) Optimization of multiple interacting ligands is disabled
 If you run Vina now with 0 or 2 or more ligands, you'll get an error, saying
that this version requires exactly one ligand.

If people have a particular need to dock multiple ligands simultaneously, please let us know and we can discuss future possibilities.

AutoDock Vina 1.0 beta 03 is distributed as binary executables for both Linux and Windows platforms (sorry, no Mac OSX version yet).  It can be downloaded from vina.scripps.edu or via links from autodock.scripps.edu.  I encourage you to try the beta version and provide feedback to us.

Thanks,

Art Olson


--
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@

Arthur J. Olson, Ph.D.
Professor
Department of Molecular Biology
The Scripps Research Institute
La Jolla, CA 92037
tel. [phone]
fax. [phone]
http://www.scripps.edu/pub/olson-web

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[bagdevi]

 Dear Olson,

I also have notices the same 180 degree rotation of the docked position from
the native docked chrystal structure. what can be the possible explanation
to this?

Regards,
Bagdevi Mishra.



On Mon, Mar 2, 2009 at 12:27 PM, Rajan75 <[hidden email]>wrote:

>
> Dear Olson,
>
> First, my heartiest congrats for this excellent version, and due
> appreciation of Oleg's hard work.
>
> Now, here is my problem:
>
> When, I bind the inhibitor to the site, I see a geometry totally opposite
> to
> that predicted. For example, if the inhibitor binds exp as A-B, I see
> binding as B-A. The position though is conserved.
>
> I am not sure, what mistake I am doing here. Please provide me some
> solution.
>
> Thanks,
>
> -Rajan
>
>
> arthur olson wrote:
> >
> > Dear AutoDock Users,
> >
> > I want to alert AutoDock users to a new beta version of Vina, which is
> > now called AutoDock Vina, a new docking code developed by Oleg Trott in
> > my lab.  AutoDock Vena uses the same format for the ligand and receptor
> > files as AutoDock4, which can be prepared by AutoDock Tools, however its
> > input is much simpler, and there is no need to run AutoGrid before
> > runing the docking.  The scoring and optimization procedures in AutoDock
> > Vina are quite different than those in AutoDock4.
> >
> > A paper announcing and describing AutoDock Vina is about to be submitted
> > for publicataion.  In the paper we compare its performance relative to
> > AutoDock4.  We have found AutoDock Vina is considerably faster than
> > AutoDock4, with comparable or better  docked structures for many
> > complexes.
> >
> > The newly released AutoDock Vina 1.0 beta 03 has the following changes
> > from the previous release:
> >
> > (1) Improved estimation of the statistical influence of the
> > flexibility of the ligand on its free energy of binding
> > (2) Optimization of multiple interacting ligands is disabled
> >  If you run Vina now with 0 or 2 or more ligands, you'll get an error,
> > saying
> > that this version requires exactly one ligand.
> >
> > If people have a particular need to dock multiple ligands simultaneously,
> > please let us know and we can discuss future possibilities.
> >
> > AutoDock Vina 1.0 beta 03 is distributed as binary executables for both
> > Linux and Windows platforms (sorry, no Mac OSX version yet).  It can be
> > downloaded from vina.scripps.edu or via links from autodock.scripps.edu.
> > I encourage you to try the beta version and provide feedback to us.
> >
> > Thanks,
> >
> > Art Olson
> >
> >
> > --
> > @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
> >
> > Arthur J. Olson, Ph.D.
> > Professor
> > Department of Molecular Biology
> > The Scripps Research Institute
> > La Jolla, CA 92037
> > tel. [phone]
> > fax. [phone]
> > http://www.scripps.edu/pub/olson-web
> >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> >
>
> --
> View this message in context:
> http://n2.nabble.com/ADL%3A-AutoDock-Vina-new-beta-release-tp2355177p2407809.html
> Sent from the AutoDock mailing list archive at Nabble.com.
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>

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