ADL: phosphate in binding site

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ADL: phosphate in binding site

FRANCESCA SPYRAKIS
Dear autodock users,
I am trying to perform a virtual screening with vina, on a protein where
the phosphate is necessary for the catalytic mechanism and it's always
present in any available protein-ligand complex.
Unfortunately i did not find the way to make vina understand that the
phosphate is there i tried to covert the file form the autodock.py plugin
but the phosphate disappeared. Then I manually copied it at the end of the
protein file but the poses obtained clearly show that the phosphate is not
considered.
Please, could somebody help me in solving this problem?
many thanks
Francesca Spyrakis

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Re: ADL: phosphate in binding site

Ruth Huey
Hi Francesca,
You can prepare your protein using AutoDockTools (http://mgltools.scripps.edu/downloads)
[either in the ADT graphical user interface or using the prepare_receptor4.py script in AutoDockTools/Utilities24...]
   
     Best wishes,
       Ruth

ps:?Which autodock.py plugin were you trying to use?
________________________________________
From: [hidden email] [[hidden email]] On Behalf Of FRANCESCA SPYRAKIS [[hidden email]]
Sent: Friday, May 09, 2014 3:18 AM
To: [hidden email]
Subject: ADL: phosphate in binding site

Dear autodock users,
I am trying to perform a virtual screening with vina, on a protein where
the phosphate is necessary for the catalytic mechanism and it's always
present in any available protein-ligand complex.
Unfortunately i did not find the way to make vina understand that the
phosphate is there i tried to covert the file form the autodock.py plugin
but the phosphate disappeared. Then I manually copied it at the end of the
protein file but the poses obtained clearly show that the phosphate is not
considered.
Please, could somebody help me in solving this problem?
many thanks
Francesca Spyrakis

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

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