Re: [rDock-list-def] rDock compilation

[Daniel Á. G. <alg...@gm...>]

Dear Elnaz,

your problem is that the ligand you are using as reference to define the
cavity in the RNA molecule is originally placed many angstroms apart. To
define a cavity using a ligand, the ligand must be inside the cavity you
want to define.

Solution: either manually displace the ligand (using pymol for instance)
inside the binding region, even the pose is not correct, and use these new
coordinates for defining the cavity; or use the Two spheres method to
define the cavity (method that does not require any reference ligand).

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Hope this helps!

Daniel



2014-05-11 13:49 GMT+02:00 elnaz mehdizadeh aghdam <ema...@ya...>:

> Dear Daniel
>
> First I should say that I sent this question to mailing list but it is being
> held until the list moderator can review it for approval. Becuse I do not
> know how much time it took I had to sent the question for you too. I am
> sorry for taking your time.
>
>
> "Dear All
> I've started to dock some RNAs with rDock. First I detach a ligand and RNA
> of a PDB file and docked them again. It maked me glad because the RMSD was
> very low and it seems rDock is a convenient program. However, when I
> started to dock my own RNAs, I came across to a strange problem. My sd
> docked files in pymol showd me that the ligand and receptor are apart from
> each other! I attached the .prm .mol2 and .sd files. It would be great if
> somebody could help."
>
>
>
> Best Regards
> Dr Elnaz Mehdizadeh Aghdam
> PharmD, PhD Student of Pharmaceutical Biotechnology
> Faculty of Pharmacy
> Tabriz University of Medical Sciences
> Tabriz
> Iran.
> Tel: +98 (411) 3372250-239
>
>
>


-- 
Daniel Álvarez | PhD Student
dan...@ub...  | www.ub.edu/cbdd
Computational Biology and Drug Discovery Group
Faculty of Pharmacy | University of Barcelona