From: Jason Swails <>
Date: Tue, 11 Aug 2015 09:39:24 -0400

On Thu, Aug 6, 2015 at 2:06 PM, Sarah Graham <> wrote:

> Hi,
> I am interested in using SPAM to compare water sites. There is a previous
> email on the mailing list stating that the and cpptraj patch for
> ambertools12 sent out by Jason Swails is the better spam version to use.
> As there isn't much documentation on SPAM in the Ambertools14 manual, I was
> wondering if this is still the preferred version or if the version included
> in ambertools14 is more recent?

​The version included in AmberTools 14 and 15 *is* more recent, but it is
still not well-automated -- it's work in progress. The suggested method
for running SPAM calculations are to use the "volmap" command in cpptraj to
identify peaks in solvent density, then feed those peaks to the "spam"
command which can be used to reorganize water molecule indices (so the same
water appears in the same site every frame) and compute an energy-shifted
electrostatic and van der Waals interaction for that water.

It then dumps a time series of energies for each water site, which you need
to post-process (using numpy and scipy, for instance) into a free energy
(from which you can back-out the enthalpy and entropy). The code in provides code for turning this energy time-series into free
energies, although relies on a patched cpptraj from AmberTools
12​. You can use that as a template. Hopefully can be updated to
work with the latest version of AmberTools and automate the part of the
procedure that cpptraj doesn't yet.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Aug 11 2015 - 07:00:04 PDT
Custom Search