Re: Can amber calculate the gibbs perturb energy when a ligand added a group

From: Bill Ross <>
Date: Sat 13 Oct 2001 21:50:14 -0700 (PDT)

        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

        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
Custom Search