ADL: autodock Digest, Vol 98, Issue 2

corrjose at gmail.com corrjose at gmail.com
Sat Oct 6 12:11:34 PDT 2012


You need to sample the natural or reported ligand, if it is, try increasing to 80, however, the most important is the binding pose, to get free energy values you can use other computer procedures. I hope it helps you.
Best wishes
Jose correa
Enviado desde mi oficina móvil BlackBerry® de Telcel

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Subject: autodock Digest, Vol 98, Issue 2

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Today's Topics:

   1.  large energy at pocket (aman36)


----------------------------------------------------------------------

Message: 1
Date: Sat, 6 Oct 2012 05:11:37 -0700 (PDT)
From: aman36 <amnakhan369 at gmail.com>
Subject: ADL: large energy at pocket
To: autodock at scripps.edu
Message-ID: <1349525497713-7577598.post at n2.nabble.com>
Content-Type: text/plain; charset=us-ascii

hi 

i have got a problem please help

in my docking results

the receptor binds to ligand at pocket by setting the grid points to
50,50,50 and rest parameters are default
  but  the binding energy is very *large, positive energy.*

when i set the grid box to 60 60 60 , the specific binding is not achieved, 

please anybody help in this  how to get negative energy with binding at
pocket 


regards




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