AMBER Archive (2008)

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

From: David A. Case (case_at_scripps.edu)
Date: Fri Feb 22 2008 - 11:14:59 CST

On Thu, Feb 21, 2008, David Cerutti wrote:

> 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.

First, I don't understand (of the top of my head) why this would not work
with pmemd...have you tried it?

Second, are you and your advisor convinced that using restraints (i.e.
conventional umbrella sampling) is worse than SHAKE-style constraints?

...dac
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