I wish to compare the gibbs energy's change between two
ligands association of the receptor,where the two igands are
different just in a substitute group(the amount of atoms are
different).Can amber use gibbs module to do that then how to
use leap to prepare the pertubparm files where some new atoms
are added
You need to create atoms that are 'dummy' - nonexistent - in one
state, and real in the other. Probably the methane tutorial would
help.
or just calculate the two absolute free energy of
association of the receptor seperately?
This would be interesting to compare results, however if the
difference is small, it could be overwhelmed by the error in
calculating the two larger free energies.
Bill Ross
Received on Sat Oct 13 2001 - 21:50:14 PDT
