[AMBER] unique atoms in TI softcore

From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
Date: Thu, 17 Oct 2013 11:01:11 +0100


I am currently trying to find out how to determine the unique atoms for
the TI softcore approach. The manual and tutorial A9 speak of
"appearing/disappearing" atoms and my first thought was that those
would then simply be the dummy atoms in the dummy-atom
implementation. But that obviously disagrees how it is done in the

So what exactly is it? Atom types (which would mean a simple
transformation of ethane to methanol would only have one common atom
type as per the GAFF force field)? Or topological as footnote 23 in JCP
127, 214108 suggests that the softcore implementation is
dual-topology (the atoms in the methyl group in ethane to methanol would
be the common atoms)?

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Received on Thu Oct 17 2013 - 03:30:03 PDT
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