AMBER Archive (2008)

Subject: AMBER: Question: tweaking topology files to add SHAKE-constrained bonds

From: David Cerutti (
Date: Thu Feb 21 2008 - 23:37:28 CST


    I am moving on to new phases of a project, taking a 200+ ns trajectory
of a tetrameric ligand-binding protein and doing free energy perturbation
experiments with it.
    I would like to use a method my advisor devised, which is to constrain
a bond between a ligand and protein atom via SHAKE and interatively
increase the bond length with short simulations to sample the windows.
The SHAKE-constrained bond should not imply angle terms nor dihedrals,
just a bond between two atoms.
    However, I would also like to do this in PMEMD. I don't think that
PMEMD9 has this functionality, and I'm not sure about what PMEMD10 will be
able to do.
    It seems like it should be rather simple to just go into the topology
file and add the bond, though, right? I would need to tweak the exclusion
lists, and define the bond terms, but would it terribly risky to do so? I
would think that I could easily check my results to ensure that my system
was behaving properly--it doesn't seem like I could make a tiny mistake
that slipped by unnoticed when doing something like this.
    Any advice would be appreciated.

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