ADL: (no subject)

Bobby Barnett bobby.barnett at uc.edu
Wed Mar 26 11:08:50 PDT 2008


Hi,

I thought I would point out that 2I35 is a low resolution rhodopsin structure.  The beta2-adrenergic receptor file is 2RH1 with the T4 lysozyme structure.  You can remove the residues from 1002 to 1161 to eliminate the inserted protein.  Many GPCR structures are built without knowing the exact loop structures.

Bobby Barnett


---- Original message ----
>Date: Wed, 26 Mar 2008 15:26:30 +0800
>From: "qiaoyan" <qiaoyan at dicp.ac.cn>  
>Subject: ADL: (no subject)  
>To: <autodock at scripps.edu>
>
>Hi:
>
>I am now working on a GPCR system as part of my bachelor's degree. Now the
>crystal structure of beta2-adrenergic receptor can be accessed, which PDB ID
>is 2I35 in http://www.rcsb.org <http://www.rcsb.org/> . But in 2I35, the
>third internal loop is substituted by T4L protein in order to achieve a
>better crystallization.I wang to remove the T4L.let the    the protein with
>the absence of the third loop to dock to the carazolol-a partial inverse
>anatagonist.there is an error:autogrid4.warning:Found an H bonding atom with
>thre  bonded atoms,atom series nunmber 676.
>
>Another question:how big the grid box should be ?when I use the intergal
>protein,everything went fine until it begin to dock,
>
>eval.cc:  ERROR!  energy is infinite!I don't understand why,please help
>me.thank you for your attention.
>
>________________________________________________
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Bobby L. Barnett PhD
Department of Chemistry
University of Cincinnati
PO Box 210172
301 Clifton Court
Cincinnati, OH 45221-0172
Phone:(513)556-9230 Lab:(513)556-9214
FAX:(513)556-9239


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