Re: [AMBER] strip_mask issue

From: Jason Swails <>
Date: Mon, 25 Nov 2013 18:08:35 -0500

On Mon, Nov 25, 2013 at 3:24 PM, <> wrote:

> Dear Amber,
> Since we would like to strip any atoms in the area of larger than 20 A of
> the ligand in entropy calculation to save computational costs, we use the
> *strip_mask* flag in

This won't work in general, since each frame may have a different set of
residues that satisfy the cutoff. Therefore, each frame would technically
need a different set of topology files.

Even so, the Python mask parser used by and ParmEd does not yet
accept distance-based selections. You would need to use cpptraj to create
the trajectory and matching topology files. (The mask selection is set
based on the first or reference frame in cpptraj, so it will be the same
for every frame even if it does not strictly satisfy the criteria for every

More importantly, though, is that does not really support what
you want to do. The only way this approach has been shown to work is if
you fix the positions of the atoms at the 'boundary' and do not allow them
to move during the minimization process. There is currently no way to do
this in You are of course welcome to try but I do not expect
that the default boundary treatment will suffice for a truncated entropy
calculation with

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Nov 25 2013 - 15:30:02 PST
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