ADL: ligand structure is getting broken

Diogo Martins diogo.stmart at gmail.com
Wed Jan 24 11:19:02 PST 2018


Hi,

It looks like pymol did not draw the bonds betwen some atoms, probably it's
just a visualization problem.

Other molecular viewers may display the same molecule correctly.

Best regards

On 24 January 2018 at 01:43, abhisek Mondal <abhisek.mndl at gmail.com> wrote:

> Hi,
>
> I'm trying to dock a ligand with a DNA. But whenever I'm saving the pdbqt
> file of the ligand from AutoDockTools, the chain is getting broken. I'm not
> being able to understand what wrong is happening in this step.
>
> Please help me out here.
> Ligand file: https://drive.google.com/file/d/
> 1sTiu2KEcfVwQBqXqibCCY0q0jh023
> 7dl/view?usp=sharing
>
> Image file of broken .pdbqt:
> https://drive.google.com/file/d/1UXuTbRwNA_-AaAfEagLmgItzjgF3i5wp/view?
> usp=sharing
>
>
> Thank you.
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>


More information about the autodock mailing list