Re: [AMBER-Developers] Discussion: CPPTRAJ: AT12 updated manual issue

From: David A Case <>
Date: Wed, 29 Aug 2012 16:34:55 -0400

On Wed, Aug 29, 2012, Daniel Roe wrote:
> It appears the AT12 manual was updated from the master branch
> post-release, so lots of the functionality I was adding to cpptraj
> (and documenting) after the official release made it into the manual.
> Unfortunately, this has led to situations like the one today, where a
> user tries to use a documented function that is not actually present
> in the code. I can see this being rectified one of four ways:
> 1) The simplest(?) thing may be to correct the manual and post
> something about it on the mailing list.

The master branch manual should not have put on the web site
(or the tar file). I think I was responsible for this, (although as I
remember, Ross pushed for it), but I didn't think things through enough,
somehow thinking that only fixes (and not extensions) had been added to the

Does the AmberTools tarfile at the web site have the version with the extra
cpptraj commands? How about the version at

If there are only a few cpptraj things that are not supported, we could just
update the table at to point out the problem.
It's also easy to revert; harder to fix
the problem if it's in the tarball.

> 3) Release an updated cpptraj by itself,

I'm less enthused about this, mainly because we then have multiple versions
of cpptraj out in the wild, and it adds to the general confusion. Plus,
however good Dan is, I'd like things to get as much testing by developers
before being released as possible. I'm guesing that we will probably decide
at the next developers' meeting if and when to release an AmberTools12.1.


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Received on Wed Aug 29 2012 - 14:00:05 PDT
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