Another question about interpreting parameter files. The format documentation at
http://ambermd.org/formats.html includes the following comment:
"Important note: all general type improper dihedrals (e.g. x -x -ct-hc) should appear before all specifics (ct-ct-ct-hc) in the parm list. Otherwise the generals will override the
specific with no warning."
That sounds straightforward: later definitions override earlier ones, and all general definitions should come before all specific ones. But when I look in frcmod.ff99SBildn I see the exact opposite: the general definitions come AFTER the specific ones. Does this really mean the general definitions are intended to override the specific ones? That seems very unlikely. Is this a bug? Or is the documentation incorrect, and AMBER actually uses a different rule for deciding which definition to use? If so, what is that rule?
Peter
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Received on Tue Oct 04 2011 - 10:30:03 PDT
