Dear Dr Kalju:

Thanks very much for your interest,

My question is just about the motiva= tion of curiosity when I saw that on VEGAZZ

I understand your answer when reading about fo= rce field , and now I became aware of MGL tools for p= reparation to autodock and arguslab .

I am very interested to see your Literature = but unfortunately I cannot log on the site Just in drug des= ign and using of QM, MM (oniom).

Thanks,

--- On Sun, 9/6/09, Kalju Kahn kalju*|*chem.ucsb.edu <own= er-chemistry{:}ccl.net> wrote:

From: Kalju Kahn kalju*|*chem.ucsb.edu <owner-= chemistry{:}ccl.net>
Subject: CCL: Steps of docking
To: "Ghazal, Bas= ma " <basmaghazal{:}ymail.com>
Date: Sunday, September 6, 20= 09, 7:33 PM

Sent to CCL by: "Kalju Kahn" [kalju%a%chem.ucsb.= edu]
Basma,

> Hi,
> Thanks for the first result but I re= ad that I have to add hydrogen then,
> remove the polar one coul= d you explain that please.

You're welcome! But I am not sure w= hat you are referring to this time.
In order to calculate the electrost= atic potential w/ all-atom force field
such as AMBER, you need to add al= l hydrogen atoms; these are commonly
missing in protein X-ray structures= . Addition of hydrogens to tetrahedral
carbons is trivial but addi= tion of polar hydrogens is trickier: one may
want to optimize the H-bond= ing network. Many docking programs do that
during the "protein pre= paration" stage.

In some cases you also need a structure without hyd= rogens. For example, in
UCSF Dock, you generate the protein surfac= e so that the binding pocket
could be defined. I guess eliminating H prior to surface definition saves
some computational time= . Maybe you want to ask help from AutoDock
mailing list= at http://autodock.scripps.edu/mailing_list if this is
Aut= oDock specific.

Kalju

> --- On Sun, 8/30/09, Kalju Kah= n kalju() chem.ucsb.edu
> <owner-chemistry[#]ccl.net> wrote:>
>
>> From: Kalju Kahn kalju() chem.ucsb.edu <owner-= chemistry[#]ccl.net>
> Subject: CCL: Steps of docking
> To: = "Ghazal, Basma " <basmaghazal[#]ymail.com>
> Date: Sunday, Augu= st 30, 2009, 8:26 PM
>
>
>
> Sent to CCL by: "Kalju= Kahn" [kalju]=3D[chem.ucsb.edu]
> Basma,
>
> One reason = would be that the experimental structure was crystallized with
> a sm= all ligand in a larger pocket, and the voids of that pocket contain
> water molecules. But you may want these voids be accessible to ligan= d
> atoms while docking. With standard docking methods, the wat= er will not be
> "squeezed" out during binding, as would happen with = real molecules, so you
> need to remove them. Of course, other = times you may want to keep some of
> these waters in order to benefit= from solvent-mediated interactions.
>
> Kalju
>
><= BR>>> Hi:
>> Thanks for this result but I need to ask about = somthing;
>> Why we remove water?
>> Thanks
>
&g= t;
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Dr. Kalju Kahn
>= Department of Chemistry and Biochemistry
> UC Santa Barbara, CA 9310= 6
>

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kalju Kah= n
Department of Chemistry and Biochemistry
UC Santa Barbara, CA 93106=

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