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uname -a
ls -l $X3DNA/bin/find_pair
uname -a:So you are using a 64-bit Linux machine.
Linux greentail.wesleyan.edu 2.6.18-194.el5 #1 SMP Tue Mar 16 21:52:39 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
ls -l $X3DNA/bin/find_pair:However, the file size "437552" of the find_pair command corresponds to the macosx-intel version. The linux-64bit find_pair version should have a size of "408859" as I have just checked. So I suspect you have somehow installed x3dna-v2.1-macosx-intel.tar.gz on your linux-64bit machine.
-rwxr-xr-x 1 wwang02 s16 437552 Jul 9 11:33 /home/wwang02/x3dna-v2.1/bin/find_pair
Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.