Re: [AMBER-Developers] AmberTools12.lyx broken?

From: Benjamin D Madej <>
Date: Sat, 23 Mar 2013 02:17:33 +0000

Hi all,

Is it safe to edit the AmberTools12.lyx file from the current version? I'd like to make a few last minute changes to a section I added a few weeks ago.

Ben Madej
Walker Molecular Dynamics Lab
From: David A Case []
Sent: Friday, March 22, 2013 7:11 PM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] AmberTools12.lyx broken?

On Fri, Mar 22, 2013, Daniel Roe wrote:
> AmberTools12.lyx is currently broken for me. Does anyone else have
> trouble opening it?

In spite of Robin's comments, the current head (56b3312b54b6dd257a) certainly
appears broken to me. Here is the top of the git log:

commit 56b3312b54b6dd257ad97239ac6af4a7f71e7a03
Merge: ec8a9c1 783d894
Author: Robin Betz <>
Date: Fri Mar 22 16:43:46 2013 -0700

    Merge branch 'master' of

commit ec8a9c14bdb2e92006cdf6b3e6a4102a9f879d53
Author: Robin Betz <>
Date: Fri Mar 22 16:43:21 2013 -0700

    Paramfit documentation update and addition of forces options in the

commit 197ec2d0c60b29c7c926c58b7109af8291ead826
Author: wmsmith <>
Date: Fri Mar 22 12:44:12 2013 -0700

    Updated AmberTools Manual sections



commit 1bee62dab5ccc8239e3302088b5939538b9aabf5
Author: wmsmith <>
Date: Fri Mar 22 11:49:26 2013 -0700

    Updated AmberTools documentation for new pbsa features
    -epsmemb to control membrane dielectric
    -piccg conditioned version of periodic conjugate gradient solver
    -updated implicit membrane example section

commit a1fb1359e326dddb1daa87a8f566b9895af7a30d
Author: Daniel R. Roe <>
Date: Fri Mar 22 09:14:39 2013 -0600

    DRR: Add documentation for the cpptraj action 'stfcdiffusion'.

The conflicts noted above (at 197ec2d0c60b29c7c926) indeed broke the file, but
ec8a9c14bdb2e92006cdf looks OK. Hence, I placed that version at the head of

Robin, Wes, Dan: please check to see if things are missing or broken.


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