ADL: autodock Digest, Vol 116, Issue 12

Javeed ahmad javeedahmadwar at yahoo.com
Mon Apr 14 18:03:27 PDT 2014


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, "autodock-request at scripps.edu" <autodock-request at scripps.edu> wrote:
 
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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 <f_ghasemi_82 at yahoo.com>
Subject: ADL: Cut the protein
To: autodock at scripps.edu
Message-ID:
    <1397420837.22887.YahooMailBasic at web142505.mail.bf1.yahoo.com>
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" <casado at mcmaster.ca>
Subject: ADL: Hydrogen bonds - Unexperienced user
To: "autodock at scripps.edu" <autodock at scripps.edu>
Message-ID:
    <A03325B71ECD8346982724AD3AA37E6860A2841A at FHSDB1-2.csu.mcmaster.ca>
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 <javeedahmadwar at yahoo.com>
Subject: ADL: spacing in config file
To: "autodock at scripps.edu" <autodock at scripps.edu>
Message-ID:
    <1397471610.74859.YahooMailNeo at web142606.mail.bf1.yahoo.com>
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 <juan.munoz-garcia at bioch.ox.ac.uk>
Subject: ADL: Vina: docking results dependent on ligand input
    conformation?
To: "autodock at scripps.edu" <autodock at scripps.edu>
Message-ID: <456AEB4C-2733-445D-88B4-6AA02848770D at bioch.ox.ac.uk>
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
juan.munoz-garcia at bioch.ox.ac.uk






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

Message: 5
Date: Mon, 14 Apr 2014 08:53:12 -0700
From: Ruth Huey <rhuey at scripps.edu>
Subject: Re: ADL: Dock heme to P450,    then re-use best structure to
    dock ligand
To: "autodock at scripps.edu" <autodock at scripps.edu>
Message-ID:
    <67033A0806429D469359E35EECA1B2DC01CE81B9DD1F at EXCH-CCR01.lj.ad.scripps.edu>
    
Content-Type: text/plain; charset="us-ascii"

Hi,
________________________________________
From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] On Behalf Of Oleg Trott [trott at scripps.edu]
Sent: Saturday, April 12, 2014 7:21 PM
To: autodock at scripps.edu
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 <trott at scripps.edu> 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 <adriaan.vanheule at ugent.be> 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 <trott at scripps.edu>
Subject: Re: ADL: Vina: docking results dependent on ligand input
    conformation?
To: autodock at scripps.edu
Message-ID:
    <CAHgi0UgyuS_4niMp=bb2vA1GgGOr_fgmT0w3bk9_qyM1jc4FjQ at mail.gmail.com>
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
<juan.munoz-garcia at bioch.ox.ac.uk> 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
> juan.munoz-garcia at bioch.ox.ac.uk
>
>
>
>
> ________________________________________________
> --- 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 <trott at scripps.edu>
Subject: Re: ADL: spacing in config file
To: autodock at scripps.edu
Message-ID:
    <CAHgi0Uj8+W_3qqyc+4Vp1i_M9r7oADphVzhkdwYysbZi5PF=gw at mail.gmail.com>
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 <javeedahmadwar at yahoo.com> 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/ ---

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