Re: [AMBER-Developers] amber11-with-patches

From: Jason Swails <>
Date: Thu, 10 Mar 2011 10:31:51 -0800

I think this is actually fairly straightforward:

On Thu, Mar 10, 2011 at 10:19 AM, Mark Williamson <> wrote:

> On 10/03/2011 04:06, Jason Swails wrote:
> > Hello,
> >
> > Just a quick question -- is this branch up-to-date with all of the
> patches?
> As far as I can tell, yes. Scott created this branch and brought it up
> to date. The amber11 branch is now obsolete.

Yea, I realized that after I dug a little bit (I jumped the gun a little
with the email).

> > i.e. can I create a patch against this tree for the recent sleap bugfix?
> > Have we decided this is what we're doing for bugfixes now? (If so that
> would
> I'm still unclear on this.... currently the amber11-with-patches
> contains bugfixes for both the amber11 tree and at14. I'm not sure how
> this is going to work with future bugs and at15, since at15 will already
> contain some of the fixes that will exist in the amber11-with-patches
> branch. Also, will future bugs fixes for the amber side of the code go
> into amber11-with-patches or at15-with-patches ?

AmberTools and Amber have different bug fixes. The amber11-with-patches
tracks AmberTools 1.4 and Amber11, so all patches to those two packages are
applied to amber11-with-patches. The only thing of interest in the
at15-with-patches branch (being the only thing actually released) is
AmberTools 1.5, so any patch made for that AT1.5 should be applied to that

> > be great!) Do we need a detailed procedure written out for creating them
> > while also maintaining the integrity of that branch as it was intended?
> I can generate a howto, once we have decided how we're going to proceed.

I think you can generate a howto that details how to create a bug fix based
on the idea that *some* branch in the git tree will be properly tracking the
version you're trying to patch. This protocol will be independent of the
actual branch that you should patch against. Separately we can have a list
of branches that should be used for patches for different programs.

For instance:

amber11-with-patches: Amber11 & AmberTools 1.4
at15-with-patches: AmberTools 1.5
amber12-with-patches: Amber12 & AmberTools 1.6/2.0(?) (in the future, of

... etc.

All the best,

> Regards,
> Mark
> _______________________________________________
> AMBER-Developers mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Thu Mar 10 2011 - 11:00:04 PST
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