ADL: autodock Digest, Vol 130, Issue 6

ponjayanthi B ponjayanthibt at gmail.com
Sun Jun 14 23:45:00 PDT 2015


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:
> > > >
> > > > Send autodock mailing list submissions to
> > > >   autodock at scripps.edu
> > > >
> > > > 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
> > > >   autodock-request at scripps.edu
> > > >
> > > > You can reach the person managing the list at
> > > >   autodock-owner at scripps.edu
> > > >
> > > > When replying, please edit your Subject line so it is more specific
> > > > than "Re: Contents of autodock digest..."
> > > >
> > > >
> > > > 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


More information about the autodock mailing list