Subject: RE: CCL:AutodockTools Question

From: Robert Flight <[email-masked]>
Date: Thu, 7 Nov 2002 14:53:47 -0400

Hi Liu,

I have the same problem in my system where I have a break in the amino acid 
sequence, and I get an residue with a non-integral charge.  If the charge is 
not off by much (say less than 0.5 charge units) I just adjust the charge on 
the individual atoms of the residue so that the total charge adds up to the 
proper integer (0,1,2, whatever), this shouldnt affect the docking results too 
much if the residues are outside of the Grid box used for docking.  If you are 
using Mol2 files to prepare your receptor it is really easy to modify using a 
text editor (the PDBQS format doesnt label the individual residues).

You might also want to check the original file and make sure that the bonding 
between atoms is right, as this will also affect the charge calculation.

Hope this helps.

Cheers,

Robert

>===== Original Message From "zgleo" <[email-masked]> =====
>Dear CCLers,
>   		I'm using AutoDockTools.As my receptor misses about 20 residues in the 
middle region(but far away from my pocket),it looks like owning two peptide 
chains.When I grid in ADT,there is such error message:"non-integer 
charge:Gly142,Val177,Lys198,Ile431".I have checked and found that these are 
exactly the four terminal residues.Then I fixed the residues by add H to 
terminal N and O.Unfortunately,the problem remains.How should I deal with such 
case?
>Best Regards!
>---------------------
>Liu Zhi-Guo
>Ph.D candidate
>Drug Design & Discovery Center
>Shanghai Institute of Materia Medica
>Shanghai,in China

********************************
Robert Flight
Masters Student
Department of Chemistry
University of New Brunswick
Fredericton, NB  Canada  E3B 6E2
e-mail: [email-masked]
 
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"What is wanted is not the will to believe but the wish to find out, which is the exact opposite." -- Bertrand Russell