ADL: autodock Digest, Vol 130, Issue 6

gowri shankar gowririshankar.88 at gmail.com
Mon Jun 15 04:26:43 PDT 2015


dear ponjayanthi,
         Kindly see through this link
http://mgl.scripps.edu/forum/viewtopic.php?f=9&t=2521
  if u need any help let me know..
thank you....

On Mon, Jun 15, 2015 at 12:15 PM, ponjayanthi B <ponjayanthibt at gmail.com>
wrote:

> hai all.........
>     I am very new to docking.....i am using autodock 4.2 for my
> study....while am running autodock, this showing an error that too much
> atoms...can't able to run....and so i tried to find active site using castp
> server....after running castp, i got five documents with certain
> information.....from this i don't know how to retrieve the information
> regarding the pockets and how to locate the pockets in autodock....please
> help me to find the solution....
>
> On Mon, Jun 15, 2015 at 11:40 AM, gowri shankar <
> gowririshankar.88 at gmail.com
> > wrote:
>
> > Thank you yitav ill go-through it..
> >
> > On Sun, Jun 14, 2015 at 11:50 AM, yitav glantz <yitavg at gmail.com> wrote:
> >
> > > maybe this can help
> > > http://mgl.scripps.edu/forum/viewtopic.php?f=9&t=2521
> > >
> > > On Sun, Jun 14, 2015 at 7:23 AM, suniba <suniba88chemistry at gmail.com>
> > > wrote:
> > >
> > > > Hello
> > > > Open your dlg file by using analyze option in autodock. Then open
> > > > macromolecule (the protein). Now you can view conformations ranked by
> > > > energy. When the dialogue bix appears, click in & key and then click
> on
> > > > build H-bonds and show info option. You will get all the information.
> > If
> > > > you still have doubt you can ask.
> > > > Suniba
> > > > PhD Student
> > > >
> > > > Sent from my iPhone
> > > >
> > > > > On 13-Jun-2015, at 12:30 am, autodock-request at scripps.edu wrote:
> > > > >
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> > > > > Today's Topics:
> > > > >
> > > > >  1.  question (dina dehghanian)
> > > > >
> > > > >
> > > > >
> > ----------------------------------------------------------------------
> > > > >
> > > > > Message: 1
> > > > > Date: Fri, 12 Jun 2015 07:13:59 +0000 (UTC)
> > > > > From: dina dehghanian <dina.dehghanian at yahoo.com>
> > > > > Subject: ADL: question
> > > > > To: "autodock at scripps.edu" <autodock at scripps.edu>
> > > > > Message-ID:
> > > > >   <1589869071.1885217.1434093239567.JavaMail.yahoo at mail.yahoo.com>
> > > > > Content-Type: text/plain; charset=UTF-8
> > > > >
> > > > >
> > > > >
> > > > > Hi
> > > > >
> > > > > I have done docking of ligand and protein as in video tutorial
> > provided
> > > > by web site,
> > > > > and in my log file I see? just the energy affinity of some best
> > > > interaction modes of them.Which kind of other information I could get
> > > from
> > > > docking? for example about from which part protein
> > > > > is attached to the ligand? and so on.
> > > > > I see in the paper, authors get many information from docking
> > results,
> > > > but I do not know how can I
> > > > > analyzed my docking results?
> > > > > I highly appreciate if you help me
> > > > > regards
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > ------------------------------
> > > > >
> > > > > ________________________________________________
> > > > > --- ADL: AutoDock List  ---
> > > > http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
> > > > >
> > > > > End of autodock Digest, Vol 130, Issue 6
> > > > > ****************************************
> > > >
> > > > ________________________________________________
> > > > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> > ---
> > > >
> > > ________________________________________________
> > > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> ---
> > >
> >
> >
> >
> > --
> >
> > *K. Gowri Shankar *
> >
> > *Research Scholar,*
> >
> > *C/o Prof. Albin T. Fleming, Head of the Department*
> >
> > *Room No- JS04*
> >
> > *School of Life science,*
> >
> > *Department of Zoology,*
> >
> > *Loyola college,*
> >
> > *Chennai-600034,*
> >
> > *Tamil Nadu,*
> >
> > *India*
> > *PH - +91-9884239106*, +91-9176726542
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
>
>
>
> --
> Best regards,
> Ponjayanthi B
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>



-- 

*K. Gowri Shankar *

*Research Scholar,*

*C/o Prof. Albin T. Fleming, Head of the Department*

*Room No- JS04*

*School of Life science,*

*Department of Zoology,*

*Loyola college,*

*Chennai-600034,*

*Tamil Nadu,*

*India*
*PH - +91-9884239106*, +91-9176726542


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