Re: Alchemical Free Energy Perturbation

From: jsachs_at_mail.csb.yale.edu
Date: Wed Mar 01 2006 - 15:31:07 CST

I'm trying FEP for the first time with NAMD. I'm
trying to replicate the tutorial with the ala-ser-ala --> ala3 mutation
(although in my case I've blocked the ends slightly differently).

I built the dual .pdb file by hand, generated the .psf file using CHARMM, then
used alchemify to generate the new .psf file (the one I've attached).

My questions:
1.Does the coordinate file used in the NAMD script have the dual atoms? If so,
how does it differ from the .fep file?
2.Am I correct that the .fep file (with the -1,0, and 1 flags) contains all
atoms in the system? Or should it only be the resiude that is being mutated,as
you show in the tutorial?

I've attached the files I'm using. Its running, but I want to check if you
think I've gotten the protocol correct.

Thank you so much for this effort, what a wonderful help its been...

best, Jonathan N Sachs


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