Re: [AMBER-Developers] Topology file readers

From: Ross Walker <>
Date: Tue, 29 Nov 2011 13:52:07 -0800

Sorry - couldn't resist:

> -----Original Message-----
> From: []
> Sent: Tuesday, November 29, 2011 11:31 AM
> To: AMBER Developers Mailing List
> Subject: [AMBER-Developers] Topology file readers
> In the interest of making a targeted, focused discussion about an issue
> that is causing some confusion at the moment and portends to cause
> more,
> I'd like to bring up topology readers. As I see it, we should
> ultimately
> support two, or perhaps three canonized readers, one for C, C++, and
> Fortran. I argue that the differences between C, C++, and Fortran are
> sufficient to warrant different data structures for each case, and even
> if
> there were some master object file that reads the topology and then a
> series of converters to put it into different formats, there would be
> about as much code to maintain as if we had three separate readers.
> My recommendation is that we select, perhaps at the devs meeting, the
> readers that will serve in each capacity. The readers should all do
> precisely the same things, even though information will get filtered
> differently:
> - Collect contiguous arrays of charges, Lennard-Jones A and B, bond
> stiffnesses, atom names, etc.
> - Be compatible for parallel execution (i.e. read the topology file as
> ASCII text and then parse the text, so that the text can be transmitted
> through memory to other processes without having all processes trying
> to
> read directly from the disk)
> - Collect all information deemed relevant by the current standard
> - Be able to read old-style prmtops as well as "prmtop7" format, with
> automatic detection ???
> - Efficient! Clean-coded! Expandable, and robust!
> Comments welcome. At present, we'll probably need to decide amongst
> the
> readers for nab, mdgx, and ptraj, and the readers for sander and pmemd,
> perhaps cpptraj and any other C++ based code in the tree.
> Dave
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Received on Tue Nov 29 2011 - 14:00:02 PST
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