ADL: autodock Digest, Vol 106, Issue 6

Bilal Ahmad bilalahmad252 at yahoo.com
Sat Jun 8 23:34:38 PDT 2013


Download the Sdf file and open it in visulaisation program like chimera and save it in pdb formate by save as option and save it with pdb extenstion. Then dock the pdb file of ligand with receptor whatever you want.




________________________________
 From: "autodock-request at scripps.edu" <autodock-request at scripps.edu>
To: autodock at scripps.edu 
Sent: Saturday, June 8, 2013 12:00 AM
Subject: autodock Digest, Vol 106, Issue 6
 

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Today's Topics:

   1. Re:  Analyzing autodock results - Virtual Screening
      (Avisek Mukhopadhyay)
   2. Re:  PROBLEM REGARDING AUTODOCK (Avisek Mukhopadhyay)
   3.  about batch file (Saiful Alam)
   4. Re:  about batch file (Saba Ferdous)


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

Message: 1
Date: Fri, 7 Jun 2013 01:20:23 +0530
From: Avisek Mukhopadhyay <avisekmukhopadhyay4 at gmail.com>
Subject: Re: ADL: Analyzing autodock results - Virtual Screening
To: autodock at scripps.edu
Message-ID:
    <CALTMqpVOua4MVcD_ovNSxRBaK2wztiTCx6GwnRETEbzdwPi=sw at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

thanks a lot

AVISEK MUKHOPADHYAY


On Thu, Jun 6, 2013 at 9:29 PM, Gustavo Machado Alvares de Lima <
gustavo.machado.lima at usp.br> wrote:

> Hi all,
>
> I wrote a simple python code to read log files and arrange best poses
> automatically. You only have to put rank.py file in the working folder and
> run it from terminal as follows:
>
> $ python rank.py 25
>
> To select best 25 poses from your virtual screening.
> Currently, it will work perfectly for ZINC database.
>
> I hope it is useful.
>
> Best regards,
> Gustavo
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>


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

Message: 2
Date: Fri, 7 Jun 2013 01:45:59 +0530
From: Avisek Mukhopadhyay <avisekmukhopadhyay4 at gmail.com>
Subject: Re: ADL: PROBLEM REGARDING AUTODOCK
To: autodock at scripps.edu
Message-ID:
    <CALTMqpX-7Rw_5Bw_hX6r1DWSXtWYes3=HubdLO6b0q8fqECHgw at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

it is not working


On Thu, Jun 6, 2013 at 1:31 PM, Avaneesh T <avaneesh.t at gmail.com> wrote:

> The Python version you have installed is probably incompatible with
> MGL Tools 1.4.6. Try Python 2.5.
> --
> Regards
>
> On Wed, Jun 5, 2013 at 8:29 PM, Avisek Mukhopadhyay
> <avisekmukhopadhyay4 at gmail.com> wrote:
> > respected sir,
> >
> >                     i have downloaded all the requirements of autodock
> and
> > installed it properly, but it is showing problem when i want to open it.
> >
> > i have downloaded MGL TOOLS 1.4.6, PYTHON 2.4.4, CYGWIN  and installed
> > these properly in my system, but when i want to open the autodock it is
> > showing " python.exe has stopped working"
> >
> > this is my problem, please help to access autodock in my system.
> >
> > thanking you,
> >                                                                     yours
> > faithfully,
> >                                                            AVISEK
> > MUKHOPADHYAY
> >                                                             MOBILE NO-
> > 9608646433
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>
>
> --
> Regards,
> Avaneesh.T
> B.Tech Biotechnology,
> #462, Saraswathi Hostel,
> IIT Madras, Chennai
> Ph:+91 9790878438
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>


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

Message: 3
Date: Thu, 6 Jun 2013 21:49:13 -0700 (PDT)
From: Saiful Alam <hira_78646 at yahoo.com>
Subject: ADL: about batch file
To: "autodock at scripps.edu" <autodock at scripps.edu>
Message-ID:
    <1370580553.67807.YahooMailNeo at web121306.mail.ne1.yahoo.com>
Content-Type: text/plain; charset=us-ascii

hlw

i have downloaded all the ligands from pubchem.those ligands(.sdf Files) are batch files.

i hav faced problems by performing docking with these batch files.how i operate this without explicit???

can anyone help me by providing suggesion about these problem??

regards
saiful

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

Message: 4
Date: Fri, 7 Jun 2013 10:01:22 +0100
From: Saba Ferdous <saba.bsbi154 at iiu.edu.pk>
Subject: Re: ADL: about batch file
To: autodock at scripps.edu, Saiful Alam <hira_78646 at yahoo.com>
Message-ID:
    <CANTGNo7reZ=4vS58s2AbHwzYey23xyWD4FcNVExqqY+wDWDPPA at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Just get one sdf file and perform docking with that only. And you can do
this by opening this sdf file in different visualization softwares like
Chimera and Pymol and by just using Save As option. Save them as mol2 or
pdb format and here you go...

Hope this help..
Best regards,



On Fri, Jun 7, 2013 at 5:49 AM, Saiful Alam <hira_78646 at yahoo.com> wrote:

> hlw
>
> i have downloaded all the ligands from pubchem.those ligands(.sdf Files)
> are batch files.
>
> i hav faced problems by performing docking with these batch files.how i
> operate this without explicit???
>
> can anyone help me by providing suggesion about these problem??
>
> regards
> saiful
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>



-- 
Saba Ferdous
M.Phil Bioinformatics-QAU


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

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