Re: [AMBER-Developers] Amber release names

From: Ross Walker <>
Date: Sun, 22 Feb 2015 16:21:28 -0800

> On Sun, Feb 22, 2015 at 12:45:05AM -0500, Jason Swails wrote:
>>> On Feb 21, 2015, at 10:52 AM, David A Case <> wrote:
>>> On Sat, Feb 21, 2015, Gerald Monard wrote:
>>>> No odd numbers anymore. It also leaves some
>>>> time (until the '16 release) to re-factor the directories and decide if
>>>> we drop the AmberTools naming.
>>> A couple of points along this thread:
>>> 1. We can't merge the AmberTools and Amber source trees together. The
>>> split between the AmberTools stuff and the pmemd stuff is there because
>>> they fall under different licenses. Intermingling the trees would just
>>> confuse that issue.
> This does not make sense. pmemd has its own source directory and license
> file as do some other programs (and as ~every program once did before
> Dave rearranged things years ago):
> src/pmemd/src/copyright.i
> AmberTools/src/cpptraj/LICENSE
> AmberTools/src/reduce/LICENSE
> ...
> Please provide a syllogism that explains the split.

Indeed this also makes no sense to me. The whole FREE GPL blah vs proprietary split between AmberTools and Amber was never properly done anyway. E.g. $AMBERHOME/AmberTools/src/chamber/copyright.h

! AMBER **
! **
! Copyright (c) 2003 **
! Regents of the University of California **
! All Rights Reserved. **
! **
! This software provided pursuant to a license agreement containing **
! restrictions on its disclosure, duplication, and use. This software **
! contains confidential and proprietary information, and may not be **
! extracted or distributed, in whole or in part, for any purpose **
! whatsoever, without the express written permission of the authors. **
! This notice, and the associated author list, must be attached to **
! all copies, or extracts, of this software. Any additional **
! restrictions set forth in the license agreement also apply to this **
! software. **

Says nothing about openSource / GPL etc. So the ONLY difference between stuff released as AmberTools and Amber is that the former we choose to let people use free of charge and the later we charge a fee for.

>> I agree. This is probably one of the more important distinctions we make. For people that just want to *use* Amber, it doesn't *really* matter where the source code lives... all the programs get dumped to the same place, anyway. The people that actually care about the source code directory structure are probably more likely to try modifying it and therefore probably care more about licensing issues.
> Yes, this matters to people that actually care about the source code
> directory structure - namely, developers.
> I have tried and never understood this AmberTools split.
> Others also do not understand it.
> Consequently, the split continues to appear arbitrary, and all recent
> explanations attempts either do not provide a sound argument or are
> 'well what we have now isnt so broken'.

Amen brother!

All the best

|\oss Walker

| Associate Research Professor |
| San Diego Supercomputer Center |
| Adjunct Associate Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Sun Feb 22 2015 - 16:30:02 PST
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