ADL: How to use atom distance as a filtering strategy

mswingle at mswingle at
Fri Oct 5 16:14:16 PDT 2007

You could use grep to extract the coordinates of the ligand atom in each conformation from the .dlg file 
and redirect the output to a text file. For example:

grep "DOCKED: ATOM     25  H   FOS     1" pp2a-flex6.dlg > ligand.txt

The text file can then be imported into a spreadsheet as space delimited data. Then use the formula

SQRT[(X1-X2)^2 + (Y1-Y2)^2 + (Z1-Z2)^2]

and the coordinates of the receptor atom to calculate the distances from the ligand atom coordinates.



----- Original Message -----
From: Hairat Sabit <hairat at>
Date: Friday, October 5, 2007 6:19 am
Subject: ADL: How to use atom distance as a filtering strategy
To: autodock at

> Dear all,I am docking potential substrates into protease pocket. I 
> want to use the distance of an atom in ligand and an atom in enzyme as 
> a filtering criteria beside docking energy; however, I do not know how 
> to auto-measure the distance of these two atoms in all the 
> conformations generated by autodock4 ? Any suggestion will be very helpful.
> Thank you in advanceHS
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