FEP calculations: defining hybrid residues

From: Satyavani Vemparala (vani_at_VITAE.CMM.UPENN.EDU)
Date: Wed Mar 24 2004 - 10:04:53 CST

I am trying to setup systems to compute the relative binding affinities of
two ligands L1 and L2 to a receptor R.

In the examples given in the tutorial on NAMD website, the dual topology
is represented through a hybrid molecule whose residue is defined in the
RTF file for CHARMM. In this hybrid molecule, there is connectivity
between initial and final states

But for my problem, the two ligands L1 and L2 are not connected, in this
case how do i define a hybrid molecule 'residue' for the CHARMM to
generate the exclusion lists?

any examples or suggestions are greatly appreciated.


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