how to make dual-hybrid topology?

From: Indrajaya (
Date: Mon Feb 13 2006 - 06:47:21 CST

Dear NAMD users,

I'm Indrajaya, student of Bandung Institute of Technology, Indonesia. I'm
using NAMD to do my research. I want to use alchemical free enery
perturbation feature in NAMD but I don't have a dual-topology hybrid of my
amino acid topology (alanine and glutamic acid). From the tutorial in NAMD
web site about setting up alchemical free energy perturbation calculation
in NAMD, it state that CHARMM can make this kind topology. Unfortunely, we
don't have CHARMM program in our laboratory. Can anybody guide me how to
make this topology without CHARMM?

Thank you very much for your attention. I'm looking forward to hearing you



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