The manuals for AmberTools 1.5 and AmberTools12 mention a temporary file, _MMPBSA_nmode.in, which is apparently created by MMPBSA.py to control Normal mode calculations by mmpbsa_py_nabnmode. (See pages 214 and 275 respectively.)
Although this file is mentioned in section 10.3.7 (Advanced Options), the file is not listed in 10.3.6 (Temporary Files) and it never appears to be created when running Normal mode calculations. Does such a file actually exist?
(I have a number of ligands which I wish to analyse using MMPBSA.py and I would like to perform Normal mode analysis on the trajectory of the complex and the trajectory of the free ligand without performing it on the free protein trajectory every time I run MMPBSA.py for each ligand.)
Thanks.
Joel Dockray
University of Leeds
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Mar 10 2013 - 06:00:05 PDT
