[Chimera-users] query regarding docking by chimera

Elaine Meng meng at cgl.ucsf.edu
Wed Feb 21 09:47:39 PST 2018

Dear Dr Effendi,
The message says some file is gzipped and cannot be read.  Is some input file of yours gzipped (name ending in .gz)?  

However, aside from that issue, I don’t understand why you are using Dock Prep anyway.  If you just want to look at the waters and co-crystallized ligand that are already in the crystal structure, there is no reason to use Dock Prep.  Just display the water and any other atoms you want to look at, for example (menu):

Select… Structure… solvent
Actions… Atoms/Bonds… show

Take a look at the “getting started” tutorial to learn how to use Chimera.

Also, Dock Prep does not do docking.  It only prepares the structure for calculations with other programs, and by default it removes all the waters.  However, Chimera does have an Autodock Vina interface that does some limited single-molecule docking using a web service:

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 20, 2018, at 12:17 PM, Juweria Shahrukh Effendi <javelightens at yahoo.com> wrote:
> Dear Daron 
> I am new to chimera, I want to check the conserved water molecules in my protein pdb and its reported co-crystalized ligand 
> as i do the dock prep complete 
> adding hydrogen, applying charge, 
> and i complete the whole steps the chimera isnt able to execute attaching the pic of both windows 
> can you please have a  look on it and guide me 
> thanks 
> With Regards
> Dr Juweria Shahrukh Effendi
> M.B:B.S, M.Phil Biochemistry,
> PhD Scholar (Computational Drug Design unit)Molecular Medicine
> Dr Panjwani Center for Molecular Medicine and Drug Research
> International Center for Chemical and Biological Sciences (ICCBS).
> Karachi

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