Re: [AMBER-Developers] bugfixes to NPRO in ff03 for at14 and a11

From: Jason Swails <>
Date: Thu, 10 Mar 2011 16:58:53 -0800

The modification may have been made in master a while ago, but they're not
present in amber11-with-patches. If the patches are submitted for Amber11
and AmberTools 1.4, then the amber11-with-patches branch will deviate from
the actual Amber11 + bugfixes and AmberTools 1.4 + bugfixes, which defeats
the purpose of that branch in the first place.

If you have a commit-id for those two patches, then you can quite easily
cherry-pick those commits into the amber11-with-patches branch and just push
that to the tree. However, in order to make creating patches and tracking
the patched amber version as easy as possible, any commit that goes into
amber11-with-patches should be turned into a published bugfix immediately,
and any bugfix that's published should be added to that branch immediately
as well (if amber11-with-patches was not used to create the patch in the
first place). At least I think that's the intent here.

All the best,

On Thu, Mar 10, 2011 at 4:37 PM, Mengjuei Hsieh <> wrote:

> What's special about these patches is that the modification has already
> been in master for a long time, so the design doesn't 100% apply to this
> case. However I do agree that there should be a reference branch for
> making the patches.
> Best,
> --
> Mengjuei Hsieh, Molecular Bio & Biochem, University of California Irvine
> On Thu, Mar 10, 2011 at 03:12:52PM -0800, Jason Swails wrote:
> > I think these should be applied to the amber11-with-patches branch in
> order
> > to maintain that branch's intended use. In fact, it's probably best to
> use
> > git diff on this branch to create the patches, as that would certainly
> > ensure compatibility.
> > All the best,
> > Jason
> > On Thu, Mar 10, 2011 at 12:08 PM, Mengjuei Hsieh <>
> wrote:
> > > Hi,
> > > Can I simply push the amber_web or ask for assistent here? :-)
> _______________________________________________
> 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 - 17:00:04 PST
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