FEP substrate transformation with common moiety

From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Fri Aug 27 2010 - 20:35:01 CDT

Dear All,

I would like to use FEP to slowly transform one substrate A, bound to a
protein in binding site X, into another substrate B bound to X, i.e. not
considering the exact free energy value of this transformation.

Initial and final substrates have a common moiety.

I see two options:
a) Define a FEP hybrid topology entry A2B with the joint common moiety
b) Simply include A and B as two separate PDB entries, restrain B to A
and to X

Could anybody kindly share their experience what option might work better?

Thank you very much,

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:05 CST