[AMBER-Developers] sqm and AmberTools 1.5

From: David A Case <case.biomaps.rutgers.edu>
Date: Thu, 10 Mar 2011 11:00:05 -0500

Hi everyone, but especially Jason, Ross, Andy:

Recent tests have shown that sqm in the current git tree is not compatible
with sander in amber11. So we have a problem with what to do in the upcoming

Here is one idea: don't upgrade sqm in AmberTools 1.5; that is, the sqm
directory in the tarball that users get would be the same as in AmberTools
1.4 (plus relevant bug-fixes). The argument is this: few people really
use sqm (yet) as a stand-alone tool. It is mostly called behind the
scenes by antechamber. I don't think(?) anything else in AmberTools
depends on sqm or libsqm. So, the plan would be to upgrade sqm at the
next release of sander.

Comments? Objections? Are there improvements in sqm that are time-critical
to get released?


[Note: there was a suggestion to have both a "new" and and "old" sqm
directory, but that seems really quite complicated to explain and actually

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Received on Thu Mar 10 2011 - 08:30:04 PST
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