ADL: writing out the docked conformation

Mary Varughese maryvj1985 at gmail.com
Thu May 10 22:16:14 PDT 2012


Hi,

Its working.
Thank you.
Do any one know the difference between merging or not merging nonpolar
hydrogen in setting up the macromolecule file.

On Thu, May 10, 2012 at 5:37 PM, Rupal Chauhan <chauhanrupal757 at gmail.com>wrote:

> Hi,
>
> This is the personal ID and m not a web-sever to solve your question.
> But, you ask the autodock related question and I know about it so i
> tell you.
> After loading the ligand.dlg file and you viewing the Conformations
> then, go to the Analyse>Conformations>Play.
> Press "&" button on play conformation widget
> Click "Write Complex" (Save complex.pdbqt)
> Delete all molecules from viewer.
> Now,
> File>Read molecule>complex.pdbqt
> File>Save>Write PDB (Save complex.pdb)
> ok.
>
> -Rupal Chauhan
>
> On 5/10/12, Mary Varughese <maryvj1985 at gmail.com> wrote:
> > Hi,
> >
> > After loading the ligand.dlg file & the protein structure and viewing the
> > conformations how can i write the docked complex as a pdb file. When
> tried
> > to save the ligand-protein complex it says cannot be saved, more than
> than
> > one molecules are there. Then how can i write out the pdb.
> >
> > Thanking you
> > --
> > Mary Varughese
> > Research Scholar
> > School of Pure and Applied Physics
> > Mahatma Gandhi University
> > India
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> ________________________________________________
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>



-- 
Mary Varughese
Research Scholar
School of Pure and Applied Physics
Mahatma Gandhi University
India


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