Re: ADL: autodock Digest, Vol 116, Issue 12

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

Re: ADL: autodock Digest, Vol 116, Issue 12

Javeed ahmad
when we define the grid size in ADT, the spacing option is there, and changing it changes the size of the grid box? I wonder what is it for, if we finally don't include it in config file?
 
Javeed Ahmad War
DST INSPIRE Fellow
Ph.D. Research Scholar,
Department of Chemistry,
Dr. Hari Singh Gour University,
(A Central University),
Sagar, M.P., India-470003
On Tuesday, April 15, 2014 3:01 AM, "[hidden email]" <[hidden email]> wrote:
 
Send autodock mailing list submissions to
    [hidden email]

To subscribe or unsubscribe via the World Wide Web, visit
    http://mgldev.scripps.edu/mailman/listinfo/autodock
or, via email, send a message with subject or body 'help' to
    [hidden email]

You can reach the person managing the list at
    [hidden email]

When replying, please edit your Subject line so it is more specific
than "Re: Contents of autodock digest..."


Today's Topics:

   1.  Cut the protein (fahimeh ghasemi)
   2.  Hydrogen bonds - Unexperienced user (Casado, Fanny)
   3.  spacing in config file (Javeed ahmad)
   4.  Vina: docking results dependent on ligand input
      conformation? (Juan Munoz-Garcia)
   5. Re:  Dock heme to P450,    then re-use best structure to dock
      ligand (Ruth Huey)
   6. Re:  Vina: docking results dependent on ligand input
      conformation? (Oleg Trott)
   7. Re:  spacing in config file (Oleg Trott)


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

Message: 1
Date: Sun, 13 Apr 2014 13:27:17 -0700 (PDT)
From: fahimeh ghasemi <[hidden email]>
Subject: ADL: Cut the protein
To: [hidden email]
Message-ID:
    <[hidden email]>
Content-Type: text/plain; charset=us-ascii

Dear All

I am facing difficulty in docking. How can I cut the piece of protein for example I want to separate protein in two pieces.

Best  Regards

F.Ghasemi


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

Message: 2
Date: Sun, 13 Apr 2014 21:41:19 +0000
From: "Casado, Fanny" <[hidden email]>
Subject: ADL: Hydrogen bonds - Unexperienced user
To: "[hidden email]" <[hidden email]>
Message-ID:
    <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"


   Hello,
   I have exported the sdf of a small molecule to pdb but the hydrogens and
   other bonds are rearranged. Any suggestions on how to solve this issue?
   Thank you,
   Fanny


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

Message: 3
Date: Mon, 14 Apr 2014 03:33:30 -0700 (PDT)
From: Javeed ahmad <[hidden email]>
Subject: ADL: spacing in config file
To: "[hidden email]" <[hidden email]>
Message-ID:
    <[hidden email]>
Content-Type: text/plain; charset=iso-8859-1

Greetings everyone,?
While we define the grid size in Autodock Vina, there is a parameter called Spacing(in Angstrom). I don't know where to fit that value while writing a config.txt file, If we don't need to put that in the .txt file then what is the default value of the spacing for the grid.?
Regards
?
Javeed Ahmad War
DST INSPIRE Fellow
Ph.D. Research Scholar,
Department of Chemistry,
Dr. Hari Singh Gour University,
(A Central University),
Sagar, M.P., India-470003

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

Message: 4
Date: Mon, 14 Apr 2014 12:03:32 +0000
From: Juan Munoz-Garcia <[hidden email]>
Subject: ADL: Vina: docking results dependent on ligand input
    conformation?
To: "[hidden email]" <[hidden email]>
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="Windows-1252"

Hi,

could any of the experts of Autodock Vina please tell me if they?ve seen any dependencies of docking results on the input conformation of the ligand? I?ve seen this with other scoring functions, specially for known low affinity ligands, so that to minimise this effect I submitted and ensemble of randomly generated conformations of each ligand. Would you suggest to do the same with Vina?

Thank you.
Regards.

Juan C. Munoz-Garcia, PhD
Biomembrane Structure Unit
University of Oxford   
South Parks Road
Oxford OX1 3QU
[hidden email]






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

Message: 5
Date: Mon, 14 Apr 2014 08:53:12 -0700
From: Ruth Huey <[hidden email]>
Subject: Re: ADL: Dock heme to P450,    then re-use best structure to
    dock ligand
To: "[hidden email]" <[hidden email]>
Message-ID:
    <[hidden email]>
   
Content-Type: text/plain; charset="us-ascii"

Hi,
________________________________________
From: [hidden email] [[hidden email]] On Behalf Of Oleg Trott [[hidden email]]
Sent: Saturday, April 12, 2014 7:21 PM
To: [hidden email]
Subject: Re: Dock heme to P450, then re-use best structure to dock ligand

Sorry, it looks like I misread your original post.

I hope Ruth will comment on how to combine the receptor and the ligand
in ADT. In the worst case, one can do it by hand (by editing the
files).

Oleg

On Sat, Apr 12, 2014 at 11:58 AM, Oleg Trott <[hidden email]> wrote:
> Hi
>
> You probably want to dock the cofactor first, merge it with the
> receptor to form a new "receptor", and then dock your ligand to the
> resulting structure.
>
Don't use ADT for this.
Instead, use a text editor to add just the ATOM/HETATM records from the docked cofactor pdbqt file to the receptor pdbqt file.
Then use the augmented pdbqt file as the receptor for your docking (without any further processing in ADT).

-Ruth 

> More ambitiously, you might repeat the process with cofactor binding
> modes number 2, 3, ...
also possible!

> Oleg
>
> On Sat, Apr 12, 2014 at 11:25 AM, AVanheule <[hidden email]> wrote:
>> Hi everyone,
>>
>> I have a P450 monooxygenase that I would like to use in docking. The
>> structure that I have does not include the heme group. I have carried out
>> two seperate dockings: I docked my heme group to my receptor, and I docked
>> my ligand to my receptor. Unfortunately, when I combine those results they
>> don't really make a lot of sense. They are perfectly in the same active site
>> cavity, but there are minor overlaps. I figure that I should find a way to
>> include the ideal docked state of my heme group (reassuringly, the
>> differences between the different heme conformations are minimal, and
>> literature suggests that this docking is correct) in my receptor structure,
>> THEN use that new structure to dock my ligand.
>>
>> I have been able to combine my receptor structure and my best heme docking
>> in one pdb file without problems, but the trouble starts when I read that
>> pdb file in AutodockTools to create my new .pdbqt file for the second round
>> of docking (with the ligand). Is this not the correct approach? How should I
>> go about this?
>>
>> Thank you for any help,
>> Kind regards
>> Adriaan
>>
>>
>>
>> --
>> View this message in context: http://autodock.1369657.n2.nabble.com/Dock-heme-to-P450-then-re-use-best-structure-to-dock-ligand-tp7578518.html
>> Sent from the AutoDock mailing list archive at Nabble.com.
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>
>
> --
> Oleg Trott, Ph.D. (Columbia University)
>
> Staff Scientist in the Olson Lab
> The Scripps Research Institute
>
> http://olegtrott.com



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

Staff Scientist in the Olson Lab
The Scripps Research Institute

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



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

Message: 6
Date: Mon, 14 Apr 2014 09:44:46 -0700
From: Oleg Trott <[hidden email]>
Subject: Re: ADL: Vina: docking results dependent on ligand input
    conformation?
To: [hidden email]
Message-ID:
    <CAHgi0UgyuS_4niMp=[hidden email]>
Content-Type: text/plain; charset=UTF-8

Hi

The probability distribution of the results coming from Vina should
not depend on the input ligand's conformation (position, orientation
and torsions). In other words, its results should be unbiased w.r.t.
the input. (This is a quality many, if not most, docking programs
lack)

This is not quite the same as saying that the individual results do
not depend on the input, because they are merely samples from the
above distribution. These samples will depend on the random seed, and
similarly, they may be affected by any changes in the input.

Oleg

On Mon, Apr 14, 2014 at 5:03 AM, Juan Munoz-Garcia
<[hidden email]> wrote:

> Hi,
>
> could any of the experts of Autodock Vina please tell me if they?ve seen any dependencies of docking results on the input conformation of the ligand? I?ve seen this with other scoring functions, specially for known low affinity ligands, so that to minimise this effect I submitted and ensemble of randomly generated conformations of each ligand. Would you suggest to do the same with Vina?
>
> Thank you.
> Regards.
>
> Juan C. Munoz-Garcia, PhD
> Biomembrane Structure Unit
> University of Oxford
> South Parks Road
> Oxford OX1 3QU
> [hidden email]
>
>
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---



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

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com



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

Message: 7
Date: Mon, 14 Apr 2014 09:47:53 -0700
From: Oleg Trott <[hidden email]>
Subject: Re: ADL: spacing in config file
To: [hidden email]
Message-ID:
    <CAHgi0Uj8+W_3qqyc+4Vp1i_M9r7oADphVzhkdwYysbZi5PF=[hidden email]>
Content-Type: text/plain; charset=UTF-8

Hi

I'm afraid you are mistaken. There is no program option called
"spacing" in Vina.

Oleg

On Mon, Apr 14, 2014 at 3:33 AM, Javeed ahmad <[hidden email]> wrote:

> Greetings everyone,
> While we define the grid size in Autodock Vina, there is a parameter called Spacing(in Angstrom). I don't know where to fit that value while writing a config.txt file, If we don't need to put that in the .txt file then what is the default value of the spacing for the grid.
> Regards
>
> Javeed Ahmad War
> DST INSPIRE Fellow
> Ph.D. Research Scholar,
> Department of Chemistry,
> Dr. Hari Singh Gour University,
> (A Central University),
> Sagar, M.P., India-470003
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---



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

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com



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

________________________________________________
--- ADL: AutoDock List  --- http://www.scripps.edu/pub/olson-web/doc/autodock/ ---

End of autodock Digest, Vol 116, Issue 12
*****************************************
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: autodock Digest, Vol 116, Issue 12

Ruth Huey
The 'Grid Options' widget in ADT lets the user interactively define the search space for a docking either using AD4 OR Vina.
This involves setting the search space location + size.

The keywords  'spacing' and 'npts' define the size of the search space in gpf files for AutoGrid4.  
In config files for AutoDock Vina  'size_x','size_y', and 'size_z'  keywords define the search space size.

In the parameter files, each method directly specifies the x,y,z coordinates of searchspace center.
   for vina (eg 'config.txt')
       center_x   2.5
       center_y   6.5
       center_z  -7.5
   for autogrid4  (eg 'hsg1.gpf')
       gridcenter 2.5 6.5 -7.5

The spacing option is required for the AutoGrid4 calculation and is used with 'npts' to set the size of the search space.
       spacing 0.375
       npts 64 64 64  

 AutoDock Vina  uses sizes in each dimension directly. :
         size_x = 22.5
         size_y = 22.5
         size_z = 22.5

________________________________________
From: [hidden email] [[hidden email]] On Behalf Of Javeed ahmad [[hidden email]]
Sent: Monday, April 14, 2014 6:03 PM
To: [hidden email]
Subject: Re: autodock Digest, Vol 116, Issue 12

when we define the grid size in ADT, the spacing option is there, and changing it changes the size of the grid box? I wonder what is it for, if we finally don't include it in config file?

Javeed Ahmad War
DST INSPIRE Fellow
Ph.D. Research Scholar,
Department of Chemistry,
Dr. Hari Singh Gour University,
(A Central University),
Sagar, M.P., India-470003
On Tuesday, April 15, 2014 3:01 AM, "[hidden email]" <[hidden email]> wrote:

Send autodock mailing list submissions to
    [hidden email]

To subscribe or unsubscribe via the World Wide Web, visit
    http://mgldev.scripps.edu/mailman/listinfo/autodock
or, via email, send a message with subject or body 'help' to
    [hidden email]

You can reach the person managing the list at
    [hidden email]

When replying, please edit your Subject line so it is more specific
than "Re: Contents of autodock digest..."


Today's Topics:

   1.  Cut the protein (fahimeh ghasemi)
   2.  Hydrogen bonds - Unexperienced user (Casado, Fanny)
   3.  spacing in config file (Javeed ahmad)
   4.  Vina: docking results dependent on ligand input
      conformation? (Juan Munoz-Garcia)
   5. Re:  Dock heme to P450,    then re-use best structure to dock
      ligand (Ruth Huey)
   6. Re:  Vina: docking results dependent on ligand input
      conformation? (Oleg Trott)
   7. Re:  spacing in config file (Oleg Trott)


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

Message: 1
Date: Sun, 13 Apr 2014 13:27:17 -0700 (PDT)
From: fahimeh ghasemi <[hidden email]>
Subject: ADL: Cut the protein
To: [hidden email]
Message-ID:
    <[hidden email]>
Content-Type: text/plain; charset=us-ascii

Dear All

I am facing difficulty in docking. How can I cut the piece of protein for example I want to separate protein in two pieces.

Best  Regards

F.Ghasemi


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

Message: 2
Date: Sun, 13 Apr 2014 21:41:19 +0000
From: "Casado, Fanny" <[hidden email]>
Subject: ADL: Hydrogen bonds - Unexperienced user
To: "[hidden email]" <[hidden email]>
Message-ID:
    <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"


   Hello,
   I have exported the sdf of a small molecule to pdb but the hydrogens and
   other bonds are rearranged. Any suggestions on how to solve this issue?
   Thank you,
   Fanny


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

Message: 3
Date: Mon, 14 Apr 2014 03:33:30 -0700 (PDT)
From: Javeed ahmad <[hidden email]>
Subject: ADL: spacing in config file
To: "[hidden email]" <[hidden email]>
Message-ID:
    <[hidden email]>
Content-Type: text/plain; charset=iso-8859-1

Greetings everyone,?
While we define the grid size in Autodock Vina, there is a parameter called Spacing(in Angstrom). I don't know where to fit that value while writing a config.txt file, If we don't need to put that in the .txt file then what is the default value of the spacing for the grid.?
Regards
?
Javeed Ahmad War
DST INSPIRE Fellow
Ph.D. Research Scholar,
Department of Chemistry,
Dr. Hari Singh Gour University,
(A Central University),
Sagar, M.P., India-470003

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

Message: 4
Date: Mon, 14 Apr 2014 12:03:32 +0000
From: Juan Munoz-Garcia <[hidden email]>
Subject: ADL: Vina: docking results dependent on ligand input
    conformation?
To: "[hidden email]" <[hidden email]>
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="Windows-1252"

Hi,

could any of the experts of Autodock Vina please tell me if they?ve seen any dependencies of docking results on the input conformation of the ligand? I?ve seen this with other scoring functions, specially for known low affinity ligands, so that to minimise this effect I submitted and ensemble of randomly generated conformations of each ligand. Would you suggest to do the same with Vina?

Thank you.
Regards.

Juan C. Munoz-Garcia, PhD
Biomembrane Structure Unit
University of Oxford
South Parks Road
Oxford OX1 3QU
[hidden email]






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

Message: 5
Date: Mon, 14 Apr 2014 08:53:12 -0700
From: Ruth Huey <[hidden email]>
Subject: Re: ADL: Dock heme to P450,    then re-use best structure to
    dock ligand
To: "[hidden email]" <[hidden email]>
Message-ID:
    <[hidden email]>

Content-Type: text/plain; charset="us-ascii"

Hi,
________________________________________
From: [hidden email] [[hidden email]] On Behalf Of Oleg Trott [[hidden email]]
Sent: Saturday, April 12, 2014 7:21 PM
To: [hidden email]
Subject: Re: Dock heme to P450, then re-use best structure to dock ligand

Sorry, it looks like I misread your original post.

I hope Ruth will comment on how to combine the receptor and the ligand
in ADT. In the worst case, one can do it by hand (by editing the
files).

Oleg

On Sat, Apr 12, 2014 at 11:58 AM, Oleg Trott <[hidden email]> wrote:
> Hi
>
> You probably want to dock the cofactor first, merge it with the
> receptor to form a new "receptor", and then dock your ligand to the
> resulting structure.
>
Don't use ADT for this.
Instead, use a text editor to add just the ATOM/HETATM records from the docked cofactor pdbqt file to the receptor pdbqt file.
Then use the augmented pdbqt file as the receptor for your docking (without any further processing in ADT).

-Ruth

> More ambitiously, you might repeat the process with cofactor binding
> modes number 2, 3, ...
also possible!

> Oleg
>
> On Sat, Apr 12, 2014 at 11:25 AM, AVanheule <[hidden email]> wrote:
>> Hi everyone,
>>
>> I have a P450 monooxygenase that I would like to use in docking. The
>> structure that I have does not include the heme group. I have carried out
>> two seperate dockings: I docked my heme group to my receptor, and I docked
>> my ligand to my receptor. Unfortunately, when I combine those results they
>> don't really make a lot of sense. They are perfectly in the same active site
>> cavity, but there are minor overlaps. I figure that I should find a way to
>> include the ideal docked state of my heme group (reassuringly, the
>> differences between the different heme conformations are minimal, and
>> literature suggests that this docking is correct) in my receptor structure,
>> THEN use that new structure to dock my ligand.
>>
>> I have been able to combine my receptor structure and my best heme docking
>> in one pdb file without problems, but the trouble starts when I read that
>> pdb file in AutodockTools to create my new .pdbqt file for the second round
>> of docking (with the ligand). Is this not the correct approach? How should I
>> go about this?
>>
>> Thank you for any help,
>> Kind regards
>> Adriaan
>>
>>
>>
>> --
>> View this message in context: http://autodock.1369657.n2.nabble.com/Dock-heme-to-P450-then-re-use-best-structure-to-dock-ligand-tp7578518.html
>> Sent from the AutoDock mailing list archive at Nabble.com.
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>
>
> --
> Oleg Trott, Ph.D. (Columbia University)
>
> Staff Scientist in the Olson Lab
> The Scripps Research Institute
>
> http://olegtrott.com



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

Staff Scientist in the Olson Lab
The Scripps Research Institute

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



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

Message: 6
Date: Mon, 14 Apr 2014 09:44:46 -0700
From: Oleg Trott <[hidden email]>
Subject: Re: ADL: Vina: docking results dependent on ligand input
    conformation?
To: [hidden email]
Message-ID:
    <CAHgi0UgyuS_4niMp=[hidden email]>
Content-Type: text/plain; charset=UTF-8

Hi

The probability distribution of the results coming from Vina should
not depend on the input ligand's conformation (position, orientation
and torsions). In other words, its results should be unbiased w.r.t.
the input. (This is a quality many, if not most, docking programs
lack)

This is not quite the same as saying that the individual results do
not depend on the input, because they are merely samples from the
above distribution. These samples will depend on the random seed, and
similarly, they may be affected by any changes in the input.

Oleg

On Mon, Apr 14, 2014 at 5:03 AM, Juan Munoz-Garcia
<[hidden email]> wrote:

> Hi,
>
> could any of the experts of Autodock Vina please tell me if they?ve seen any dependencies of docking results on the input conformation of the ligand? I?ve seen this with other scoring functions, specially for known low affinity ligands, so that to minimise this effect I submitted and ensemble of randomly generated conformations of each ligand. Would you suggest to do the same with Vina?
>
> Thank you.
> Regards.
>
> Juan C. Munoz-Garcia, PhD
> Biomembrane Structure Unit
> University of Oxford
> South Parks Road
> Oxford OX1 3QU
> [hidden email]
>
>
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---



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

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com



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

Message: 7
Date: Mon, 14 Apr 2014 09:47:53 -0700
From: Oleg Trott <[hidden email]>
Subject: Re: ADL: spacing in config file
To: [hidden email]
Message-ID:
    <CAHgi0Uj8+W_3qqyc+4Vp1i_M9r7oADphVzhkdwYysbZi5PF=[hidden email]>
Content-Type: text/plain; charset=UTF-8

Hi

I'm afraid you are mistaken. There is no program option called
"spacing" in Vina.

Oleg

On Mon, Apr 14, 2014 at 3:33 AM, Javeed ahmad <[hidden email]> wrote:

> Greetings everyone,
> While we define the grid size in Autodock Vina, there is a parameter called Spacing(in Angstrom). I don't know where to fit that value while writing a config.txt file, If we don't need to put that in the .txt file then what is the default value of the spacing for the grid.
> Regards
>
> Javeed Ahmad War
> DST INSPIRE Fellow
> Ph.D. Research Scholar,
> Department of Chemistry,
> Dr. Hari Singh Gour University,
> (A Central University),
> Sagar, M.P., India-470003
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---



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

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com



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

________________________________________________
--- ADL: AutoDock List  --- http://www.scripps.edu/pub/olson-web/doc/autodock/ ---

End of autodock Digest, Vol 116, Issue 12
*****************************************
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

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