AMBER Archive (2009)

Subject: [AMBER] normal mode analysis

From: Hannes Wallnoefer (
Date: Mon May 04 2009 - 04:39:16 CDT


I use the script to evaluate the entropic contribution to a free
energy of binding of protein-ligand complexes in amber10. The snapshot
extraction and the minimization works fine, but when the script starts the
nmode tool the following error appears:
forrtl: severe (39): error during read, unit 53, file sanmin_com.1.restrt
The same happens with a second complex. When i use the restart files with ambpdb
there is no error message and the structures look reasonable, so i think the
restart files are ok. Also a reduction of the minimization steps to get other
restart files for nmode results in the same error.
Does anybody know what causes this file read errors, despite the files seem to
be ok?

Best regards,

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