On Mon, Aug 29, 2022, Matthew Guberman-Pfeffer via AMBER wrote:
>
>Is the following understanding right: the TI region is the set of all
>transformed atoms. The SC region is the subset of TI-region atoms that
>disappear or appear. So, in the context of an amino acid mutation, say from
>Glu to Lys, the entire residue would be in the TI region, but only the
>C_delta and beyond atoms of the sidechain need to be in the SC region. The
>non-SC region TI atoms would be linearly transformed from Glu to Lys in
>terms of their different charges, but otherwise they would remain the
>same. Is that right?
Above is correct, but may hide an additional distinction between SC atoms
and non-SC atoms:
All non-SC atoms (whether are not they are being transformed) are described
by a single set of xyz coordinates -- the so-called "single-topology" option
in much of the (older) literature.
Atoms in the SC region use a "dual topology option".
In your example, the backbone and CB/CG parts of the residue in question are
described by a single set of coordinates, even though their charges may be
changing as one goes from Glu to Lys.
For CD and beyond, there are two sets of coordinates, one set for the Glu
atoms, and a second set for the Lys atoms. Both sets of atoms are always
"present", but at the end points they don't interact with the rest of the
system, and hence are "invisible". [The Glu atoms never "see" the Lys
atoms, but each set interacts with the rest of the system, except at the
lambda endpoints.]
There is nothing that prevents you from (say) having the entire Glu and Lys
side chains be in the soft-core region. Decisions like this lead to
interesting questions about convergence of the free energy calculations.
Fortunately, there is a lot of literature to help you out.
....good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 29 2022 - 14:00:04 PDT
