ADL: autodock Digest, Vol 130, Issue 6

gowri shankar gowririshankar.88 at gmail.com
Sun Jun 14 23:10:05 PDT 2015


thank you suniba,
i think i have raised this question very long back in this forum and i have
published couple papers using AutoDock 4.5...and i am done with it..rite
now using AutoDock Vina..i would like to know is it better to use AutoDock
Vina or ill revert back to AutoDock 4.5..Bkoz rite now i am writting
results and dissussion part for my paper after using AutoDock Vina.. i
would like to have some suggestion from people who are expert in the field
of Docking..And i would like to know do u have any experience in working
with GOLD, Glide, argusLab e.t.c. will all the softwares docking energy
will be same???..which software is highly preferable to use??..And my last
question is..i have did lots of docking but none of the docking score did
not exceed more than -12.86 Kcal/mol at the maximum -15 Kcal/mol using both
AutoDock 4.5 and AutoDock vina..but i have seen in some papers it goes to
-224 kcal/mol..how can it be possible..any suggestions???

On Sun, Jun 14, 2015 at 9:53 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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> >  1.  question (dina dehghanian)
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> > ----------------------------------------------------------------------
> >
> > 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
> >
> >
> >
> >
> >
> >
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> > End of autodock Digest, Vol 130, Issue 6
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-- 

*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,*

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*India*
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