AMBER Archive (2005)

Subject: AMBER: mm_pbsa question

From: Matthew Davies (Matthew.Davies_at_jenner.ac.uk)
Date: Tue Jul 19 2005 - 05:07:51 CDT

I'm trying to calculate the affinity of a receptor for a nine residue
ligand using mm_pbsa. My question is can the calculation be broken down
to account for each individual residue's interaction with the system.
The mm_pbsa script does allow for the incorporation of multiple ligands
but it then combines them into a single structure. Is there anyway to
perform the calculation so that each ligand in the script is calculated
separately without having to generate separate topology files for each
residue?

 

Matt Davies

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