ADL: how to save docked complex pdb

german@my-elcot.de german at my-elcot.de
Fri Aug 17 04:24:21 PDT 2007


Hi!

The only way I found is to extract the structure of the ligand from the
dlg-file and convert it to a mol2-file. And then you have to load both
files (new lingand file and DNA-file) in sybyl or moe and safe this as a
pdb-File.

I don't know if AutoDock3 works with adt, there is a option, to write
every result for the ligand as an pdbqt-file.
If there is no way, to use adt with AutoDock 3, I wrote a script, that
extract the best solution from the dlg-file.
If you want, I can send it to you.

Bye

German

> hello autodock user
>
> i m new user of autodock 3
> i have docked my DNA with ligand and produced the
> result
> now want to save docked complex of DNA and ligand as
> .pdb file.
> but i m not getting any idea how it can be possible ?
> can any body suggest me the way by whick i can save my
> complex .pdb file
> i need this in urgent as i have to do free energy and
> molecular dynamics study of my docked complex.
>
>
> please help , any suggestion and help will be
> appreciated
> thanks in advance
>
> regard
> manvendra (phd) acbr, delhi, INDIA )
>
>
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