From: sem ciccioni (
Date: Mon Apr 18 2016 - 16:21:08 CDT

Dear namd Users,
I would like to approximate the free binding energy of a complex Ligand Protein of my interest through the use of the GBIS method.
I ran 3 GBIS simulations, one with the complex, one with the Protein and one with Ligand, then I extracted the potential energy from the log files.
I calculated then ΔG_bind = < G_GBSA(complex) – G_GBSA(protein) – G_GBSA(ligand).
I was told instead that I have to run an explicit MD than generate three new .dcd with the complex only the Protein only and the Ligand only.
Than run again with NAMD the dcd with the GBIS on. Do you know which modification I have to apply to the configuration file in order to do so.
Which procedure is correct? Are they equivalent?
Thanks in advance.

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