AMBER Archive (2006)

Subject: Re: AMBER: Announcement: Amber 9 is now available

From: Feng X Zhou (feng.zhou_at_abbott.com)
Date: Mon Apr 03 2006 - 10:28:48 CDT

Hello all,

Excuse me for my lack of knowledge in this field (I work mostly with
computers)... and hence this might be a totally irrelevant remark, but
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. XML is not
disk space efficient but given the amount of disk spaces available these
days, perhaps this would not be a major concern?

This may not be compatible with the format most people use today, but it
seems Bioinformatics (sequencing) people are already using XML a lot....
(for sequence data and homology studies)?

-Feng Zhou

UNIX admin, Abbott Lab

Friday, March 31, 2006 10:57 AM
To: amber_at_scripps.edu
cc:
From: "David A. Case" <case_at_scripps.edu>
Subject: Re: AMBER: Announcement: Amber 9 is now available

On Fri, Mar 31, 2006, David E. Konerding wrote:
>
> I would like to add netcdf trajectory format support to UCSF Chimera, so
> a pointer to the binary file format documentation would be very useful.
> I didn't see it in the manual.

See the "file formats" link on the Amber web page. The exact URL is here:

    http://amber.scripps.edu/netcdf/nctraj.html

>
> Have you guys given thought to using netcdf or HDF5 for prmtop files as
> well as trajectories? This would eliminate the need for custom
> parsers of the prmtop file format, and would produce much smaller prmtop
> files.

We have no such plans...we'll have to see how the trajectory stuff works.

...dac

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