AMBER Archive (2006)

Subject: AMBER: Using XML for Amber files

From: David A. Case (
Date: Tue Apr 04 2006 - 17:42:35 CDT

On Mon, Apr 03, 2006, Feng X Zhou wrote:

> could XML format be a possible future candidate for Topo, param, or even
> Coordinates?
> It would seem like a great simplifier of the parsers (if all config &
> input data is in XML), only one parser would be needed using readily
> available XML libraries and the proram just need to deal with the data
> structures rather than formats, and it is human friendly.

This comes up from time to time, but there are no current plans to go in this
direction. We generally try avoid file format changes unless there is a
strong reason to change. For one thing, no only do *we* have to write and
test new code, but many other programs that use our formats would have to do
that as well. So, the proposed benefits would have to be quite substantial.

Two other points:

a. Someone would have to do it;
b. We would have to really understand the innards of the
     "readily available XML libraries". We are already struggling with
     having Amber depend on the netCDF libraries. We have to make
     sure that our program can be ported to a very wide variety of platforms,
     including high-performance sites that don't even exist right now.
     So we can't afford to become dependent on something we don't really


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