Re: [AMBER-Developers] sqm and AmberTools 1.5

From: Andreas Goetz <>
Date: Thu, 10 Mar 2011 14:07:50 -0800

As Dave pointed out, there are not many changes to the standalone QM program sqm since AT1.4. Most changes affect QM/MM and sander. The major additions for sqm are PM3/ZnB parameters, the PM3-MAIS Hamiltonian and calculation of the dipole moment.

I would opt to distribute sqm/sqmlib from AT version 1.4. We will have to remove the test for PM3/ZnB or add PM3/ZnB, both of which is easily doable (PM3-MAIS and dipole moment only have tests for sander right now).

All the best,

On Mar 10, 2011, at 1:35 PM, Jason Swails wrote:

> So I've been playing around a little more with building AmberTools 1.5 with
> sqm from amber11-with-patches, and found an issue involved with just using
> dropping in sqm 1.4:
> Basically, sqm 1.4 knows nothing about the changes that have been done to
> configure and how config.h is now set up differently, so the make fails
> immediately with a mountain of errors. I was able to fix this by just
> dumping the revised config.h created by in $AMBERHOME/src
> into $AMBERHOME/AmberTools/src. Mostly, the changes I made were just adding
> in config.h variables used by Amber11/AT1.4 that were dumped in favor of
> more flexible versions some time ago; but I did add to some other variables
> in a way that should make no difference to 99% of users, but which
> sacrifices some of the flexibility introduced with the new suite of flags.
> To get this to work, would have to be run immediately after
> configure was run, and it would have to be modified to edit the config.h in
> $AMBERHOME/AmberTools/src as well.
> Should I modify configure in the at15-with-patches branch to automatically
> call after it's over, or just print out a warning that you
> need to run that script afterwards?
> Note that this will force to be necessary even for
> AmberTools 1.5 sans Amber11, which may be as confusing as having sqm and
> sander_qm present in the same release (?). Alternatively we could just
> modify AmberTools1.5 configure script to automatically dump out the revised
> form of the config.h file that prints, which avoids the
> issues mentioned above (but would still need to be run for
> Amber11 to properly work with AmberTools 1.5).
> Thoughts?
> Jason
> On Thu, Mar 10, 2011 at 11:32 AM, David A Case <>wrote:
>> On Thu, Mar 10, 2011, Jason Swails wrote:
>>> Not upgrading sqm will
>>> certainly fix QM/MM in sander, but then the sqm documentation and such
>> will
>>> have to be rolled back to an earlier date...
>> A key question here is: how much has really been updated in the stand-alone
>> sqm since last April? Is the problem that Jason identifies (documentation
>> changes) a serious one? Is there a reason to want to get version 1.5 of
>> the stand-alone code out there in a more timely fashion (i.e. before the
>> next
>> release of sander)?
>> My feeling from the meetings (and from monitoring code going into git) is
>> that
>> almost all recent development has been on the QM/MM side (e.g. getting
>> various
>> ab-initio codes hooked in, either directly or through PUPIL, having
>> adaptive
>> QM/MM boundaries, etc.) But if I am missing things, then Jason's
>> suggestion
>> (below) is probably the way to go. So, the sqm people need to chime in
>> here.
>>> To avoid having to sit on sqm 1.5 for another year until Amber12 is
>>> released, we can ... package sqm1.4 into a
>>> different directory that won't cause confusion (for example sander11_qm,
>> or
>>> something of the like). The only thing that would need to change is
>> where
>>> sander's Makefile has to go to build libsqm. This is a very fast, easy
>>> change to the script to get this to work.
>> ....dac
>> _______________________________________________
>> AMBER-Developers mailing list
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER-Developers mailing list

Dr. Andreas W. Goetz
San Diego Supercomputer Center
Tel  : +1-858-822-4771
Web  :
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Received on Thu Mar 10 2011 - 14:30:02 PST
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