If, hypothetically, one was to calculate the binding free energy
between two structures, (say two alpha helices or a ligand in its
binding pocket), and for this, specified an atom in both structures to
do the pulling, would this have the same effect as if the pulling was
done using the center of mass? What I mean is, if I calculated the
center of mass of structure A (hypothetical structure A) and luckily
the COM of this structure coincides to atom number ## . If I applied
the force using the COM formalism be the same as specifying that this
structure should be pulled with the spring attached to this atom?
Thank you
Fabrício
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 09 2012 - 10:30:03 PDT
