ADL: autodock Digest, Vol 87, Issue 21

Julio Dominguez acheron24 at hotmail.com
Wed Nov 30 13:27:33 PST 2011


Re: vina and restricting docking area
Care to post a link to said video? Is it at youtube.com? 
I think that there are indirect ways to "rotate" the box. I would transform the relative coordinates of the receptor. UCSF Chimera (http://www.cgl.ucsf.edu/chimera/) can do that. Just rotate the receptor then open the save PDB dialog. Before clicking OK in the save dialog, uncheck the "save untransformed coordinates" and use a different name for the PDB. Now, open both receptor files and you will see the original and rotated structures.
I hope this helps. If not, let us know.
> > plz see the ADL tutorial video> > On 30 November 2011 19:29, Phil Cunningham <phil.cunningham at kcl.ac.uk>wrote:> > > Hi> > I would like to restrict the docking region in the receptor protein> > However by specifying center x y and z AND lengths of the side> >> > this restricts my restricting to 'boxes' using the existing axes> >> > How can I twist the 'docking box' relative to the molecule axis?> >> > Phil> >> > --> > Phil Cunningham> > Senior Bioinformatics Officer> > King's College London> > 0207 848 4239 (work)> > Home Account email> >

> From: autodock-request at scripps.edu
> Subject: autodock Digest, Vol 87, Issue 21
> To: autodock at scripps.edu
> Date: Wed, 30 Nov 2011 12:00:01 -0800
> 
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> Today's Topics:
> 
>    1.  autodock4 prep. receptor with metal ions (Hong Liang)
>    2.   Warning when running autogrid and autodock
>       (Andres Felipe Vasquez Jimenez)
>    3.  Ice Structure (Nancy)
>    4. Re:  Ice Structure (Ajay Rana)
>    5.  vina and restricting docking area (Phil Cunningham)
>    6. Re:  vina and restricting docking area (Ajay Rana)
>    7. Re:  Ice Structure (Stefano Forli)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 29 Nov 2011 13:38:25 -0700
> From: Hong Liang <hongliang.dal at gmail.com>
> Subject: ADL: autodock4 prep. receptor with metal ions
> To: autodock at scripps.edu
> Message-ID:
> 	<CAD_zWnKhSgTs2jdoNJOEeMc8hb20KV-WHtH=Bvdy6kEukjxA3g at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Dear list,
> 
> Is there a practical tutorial demonstrating how to use Autodock 4 docking
> ligands into a receptor which has metal ions (such as Zn2+) in the binding
> site?
> 
> I saw a paper mentioned that,  but it did not provide enough information on
> how to prepare the acceptor,  such as protonated stage of His or other
> residues coordinated with Zn2+ ions, the bond between Zn and sidechain atom
> (existed in pdb file), etc.
> 
> Bull. Korean Chem Soc., 2010, 31(12), 3644
> 
> Thanks,
> 
> Hong
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Tue, 29 Nov 2011 17:54:15 -0500
> From: Andres Felipe Vasquez Jimenez  <af.vasquez231 at uniandes.edu.co>
> Subject: ADL:  Warning when running autogrid and autodock
> To: autodock at scripps.edu
> Message-ID: <fbf1c1042c01.4ed51c47 at uniandes.edu.co>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Tue, 29 Nov 2011 19:49:07 -0800
> From: Nancy <nancy5villa at gmail.com>
> Subject: ADL: Ice Structure
> To: AutoDock Users <autodock at scripps.edu>
> Message-ID:
> 	<CABLk=_gTPu8MvqJ0t+NhYVzCn3XEg5EfDSCOnMGG9hrUqLVQoQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi All,
> 
> I would like to perform molecular docking to an ice crystal surface;
> does anyone know if such a structure file can be obtained online?
> 
> Thanks,
> Nancy
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Wed, 30 Nov 2011 09:36:22 +0530
> From: Ajay Rana <ajay1rana at gmail.com>
> Subject: Re: ADL: Ice Structure
> To: autodock at scripps.edu
> Message-ID:
> 	<CAJfvkj=kt9o1h20E_2qMdRoN0-Bb_pV+nSTUnq9RdA127oZ0jA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> reduce the flexibilirt of groups when you generate the structurw
> 
> On 30 November 2011 09:19, Nancy <nancy5villa at gmail.com> wrote:
> 
> > Hi All,
> >
> > I would like to perform molecular docking to an ice crystal surface;
> > does anyone know if such a structure file can be obtained online?
> >
> > Thanks,
> > Nancy
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> 
> 
> 
> --
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Wed, 30 Nov 2011 13:59:43 +0000
> From: Phil Cunningham <phil.cunningham at kcl.ac.uk>
> Subject: ADL: vina and restricting docking area
> To: autodock at scripps.edu
> Message-ID: <4ED636CF.1050205 at kcl.ac.uk>
> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
> 
> Hi
> I would like to restrict the docking region  in the receptor protein
> However by specifying center x y and z AND lengths of the side
> 
> this restricts my restricting to 'boxes' using the existing axes
> 
> How can I twist the 'docking box' relative to the molecule axis?
> 
> Phil
> 
> -- 
> Phil Cunningham
> Senior Bioinformatics Officer
> King's College London
> 0207 848 4239 (work)
> Home Account email
> 
> 
> 
> 
> 
> ------------------------------
> 
> Message: 6
> Date: Wed, 30 Nov 2011 19:36:43 +0530
> From: Ajay Rana <ajay1rana at gmail.com>
> Subject: Re: ADL: vina and restricting docking area
> To: autodock at scripps.edu
> Message-ID:
> 	<CAJfvkj=Z14hZDpuqdLVQ0LmEt0nh4DUX+unhC=f1VTK6n+80Qw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> plz see the ADL tutorial video
> 
> On 30 November 2011 19:29, Phil Cunningham <phil.cunningham at kcl.ac.uk>wrote:
> 
> > Hi
> > I would like to restrict the docking region  in the receptor protein
> > However by specifying center x y and z AND lengths of the side
> >
> > this restricts my restricting to 'boxes' using the existing axes
> >
> > How can I twist the 'docking box' relative to the molecule axis?
> >
> > Phil
> >
> > --
> > Phil Cunningham
> > Senior Bioinformatics Officer
> > King's College London
> > 0207 848 4239 (work)
> > Home Account email
> >
> >
> >
> > ______________________________**__________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/**mailing_list<http://autodock.scripps.edu/mailing_list>---
> >
> 
> 
> 
> -- 
> -- 
> *Ajay Rana*
> *CSIR-SRF
> CDRI
> Lucknow
> T. No-+91-9794904319*
> *Email ID: ajay_rana at cdri.res.in*
> [image: LinkedIn] <http://in.linkedin.com/in/ajay1rana>   [image:
> Facebook]<http://www.facebook.com/profile.php?id=700203161>
>    [image: Twitter] <http://twitter.com/ajay1rana>
> 
> 
> ------------------------------
> 
> Message: 7
> Date: Wed, 30 Nov 2011 11:30:06 -0800
> From: Stefano Forli <forli at scripps.edu>
> Subject: Re: ADL: Ice Structure
> To: "autodock at scripps.edu" <autodock at scripps.edu>
> Message-ID: <4ED6843E.5060606 at scripps.edu>
> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
> 
> Hi,
> 
> by simply googling for it, I've found some potentially interesting links having PDB 
> coordinates of ice:
> 
> http://www.nyu.edu/pages/mathmol/library/water/
> http://www.edinformatics.com/interactive_molecules/ice.htm
> 
> You probably want to make an array of one these structures to create a surface big enough 
> for your ligand (by the way, I'm curious: which kind of ligand is binding on ice?)
> 
> However, to my knowledge there isn't much about docking on ice, and energy estimations are 
> assuming room temperature (298.15 K) environment.
> Also, the ice surface is rather uniform with no special features, i.e. a repetition of 
> Hb-acceptor/Hb-donor patterns in every direction.
> That said, you want to be careful about the meaning of the results...
> 
> Happy (cold) docking,
> 
> 
> Stefano
> 
> 
> 
> On 11/29/2011 07:49 PM, Nancy wrote:
> > Hi All,
> >
> > I would like to perform molecular docking to an ice crystal surface;
> > does anyone know if such a structure file can be obtained online?
> >
> > Thanks,
> > Nancy
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> 
> 
> -- 
>   Stefano Forli, PhD
> 
>   Research Associate
>   Olson Molecular Graphics Laboratory
>   Dept. Molecular Biology,  MB-112
>   The Scripps Research Institute
>   10550  North Torrey Pines Road
>   La Jolla,  CA 92037-1000,  USA.
> 
>      tel: (858) 784-2055
>      fax: (858) 784-2860
>      email: forli at scripps.edu
>      http://www.scripps.edu/~forli/
> 
> 
> ------------------------------
> 
> ________________________________________________
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> End of autodock Digest, Vol 87, Issue 21
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