[AMBER-Developers] questions about gem

From: case <case.biomaps.rutgers.edu>
Date: Mon, 21 Mar 2011 17:53:13 -0400

John, Alexey, others:

I've been looking at the gem-devel branch in git. Here are a few questions
and comments.

1. The license is GPLv2. Most of AmberTools is GPLv3. Is there a reason for
the v2 decision? Or a reason not to go to v3? Either way is OK, since gem is
a separate component, but simplicity and consistency argue for v3, unless
there is some dependency that hinders it.

2. The dependence on MSMS is understandable but to be regretted, because
MSMS is limited in licensing, and fails to produce correct results reasonably
often (at least that used to be the case). Further, I've not been able to
contact any scripps.edu domains for several days, including the download site
for MSMS. (Can anyone else succeed?)

A good challenge at the end of the README might be to find an MSMS
replacement, e.g. by modifying Paul Beroza's molsurf code to output the
required surface representation.

3. Is it likely that this is really ready for release? The Installation
instructions refer to Fedora 9 and say things don't work for Ubuntu. I'm not
trying to be critical, but wondering if we are not better off whipping this
into shape over the next few months, and adding it to the next release of
AmberTools. The current installation complexity is a step beyond other parts
of AmberTools (in terms of what one has to do before installing the program),
and it hasn't been generally used by Amber developers (so we may not be in a
good position to provide support).

Comments welcome here.


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Received on Mon Mar 21 2011 - 15:00:04 PDT
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