AMBER Archive (2006)

Subject: Re: AMBER: Ptraj syntax change Amber8->Amber9 ?

From: David A. Case (
Date: Wed Nov 22 2006 - 15:22:37 CST

On Wed, Nov 22, 2006, Markus Kaukonen wrote:
> Could the section in the manual Ptraj/Image (Pages
> 252-253 of Amber9 pdf manual) be rewritten with more examples?
> As it stands now I can't understand much of it.

I agree: reading that paragraph always leaves me completely confused. For

a. why are will still referring to SPASMS(!), and why does the "recommended
usage" include the "origin" keyword, when that is not what the "Amber
standard" is supposed to require?

b. the specification of what is required and what is optional (in the words
following "image") looks weird: the specification seems to indicate that both
"mask" strings are required, but that is not really that case.

c. it is not clear what happens if you leave out the "com <mask>" part.

Here and elsewhere, commented examples would be a real help.

(Note to all: tutorial B5 is a good addition to the manual (having a list of
common commands with fairly detailed comments), but it doesn't solve this
particular problem.)


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