ADL: (no subject)

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ADL: (no subject)

Neel Dholakia
Hello Everyone,

I came across a query while using vina. The protein- ligand interaction in
autodock tools is showing me hydrogen bond formation while there is no bond
formation when I use Vina for docking. The coordinates are the same for
both and spacing is 1 Angstrom.

any suggestion is appreciated

Thank You

Neel
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Re: ADL: (no subject)

Ruth Huey
Vina uses the presence or absence of a bonded hydrogen to assign some atom types.  
Vina does not energy-minimize the positions of hydrogen atoms (they are instead random).

For this reason, AutoDockTools does not show hydrogen bonds for Vina results.

________________________________________
From: [hidden email] [[hidden email]] On Behalf Of Neel Dholakia [[hidden email]]
Sent: Friday, July 11, 2014 6:35 AM
To: [hidden email]
Subject: ADL: (no subject)

Hello Everyone,

I came across a query while using vina. The protein- ligand interaction in
autodock tools is showing me hydrogen bond formation while there is no bond
formation when I use Vina for docking. The coordinates are the same for
both and spacing is 1 Angstrom.

any suggestion is appreciated

Thank You

Neel
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

________________________________________________
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Re: ADL: (no subject)

Neel Dholakia
So, is there any solution for this so that it is possible to visualize the
hydrogen bonds?


On Fri, Jul 11, 2014 at 9:14 PM, Ruth Huey <[hidden email]> wrote:

> Vina uses the presence or absence of a bonded hydrogen to assign some atom
> types.
> Vina does not energy-minimize the positions of hydrogen atoms (they are
> instead random).
>
> For this reason, AutoDockTools does not show hydrogen bonds for Vina
> results.
>
> ________________________________________
> From: [hidden email] [[hidden email]] On
> Behalf Of Neel Dholakia [[hidden email]]
> Sent: Friday, July 11, 2014 6:35 AM
> To: [hidden email]
> Subject: ADL: (no subject)
>
> Hello Everyone,
>
> I came across a query while using vina. The protein- ligand interaction in
> autodock tools is showing me hydrogen bond formation while there is no bond
> formation when I use Vina for docking. The coordinates are the same for
> both and spacing is 1 Angstrom.
>
> any suggestion is appreciated
>
> Thank You
>
> Neel
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---