ADL: Query Regarding Analysis of Autodock Vina Results

sai nitin sainitin7 at gmail.com
Thu May 17 13:46:32 PDT 2012


Hi preeti,

Check this link...follow the procedure make complex of protein and ligand
and visualize in pymol

http://autodock.scripps.edu/faqs-help/faq/is-there-a-way-to-save-a-protein-ligand-complex-as-a-pdb-file-in-autodock/?searchterm=complex


Use linux OS these commands works in this OS... then exactly see how ligand
bound to protein using pymol u can do many things as hydrogen bonds so on...

Best
Nitin

On Thu, May 17, 2012 at 11:35 AM, Preeti Singh <singhpreeti236 at gmail.com>wrote:

> Respected Sir,
>
> I am Preeti Singh from CSIR-IICT, India. I am using your Autodock Vina for
> Virtual Screening of my Ligands.
> I am getting the Binding Affinity values given in Log file and also I am
> getting the Out.pdbqt files. But could you please tell me how should I
> analyse the interaction betwwen the protein and the ligand..? how can I
> visualise the interaction between my protein's active site and Ligand bind
> to it..?
> Please help me out.
>
> Awaiting your response
>
> Sincerely,
> *Regards*
> *Preeti Singh*
> *ACB student,*
> *IICT(CSIR), Hyderabad*
> *INDIA*
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>



-- 

Sainitin D
PhD student
Bioinformatics Group
Biotechnology Center
Technische Universität Dresden
Tatzberg 47/49
01307 Dresden, Germany
Tel Lab:+49 (0)351 463 40060


More information about the autodock mailing list