On May 17, 2012, at 6:08 PM, B. Lachele Foley wrote:
> Sorry I haven't weighed in before now. I haven't read all bits of
> the conversation either. Apologies if I duplicate. (many hardware
> failures lately)
>
> The only thing to be wary of with using sleap is that it might still
> be a bit buggy. We like what sleap was trying to do. We just kept
> having trouble building files with sleap and gave up. Granted,
> there are issues in tleap, but those are long known, and we had
> already learned to deal with them.
Sleap has worked okay for my purposes, but I know the problems you
mention are real.
> We finally made our own builder. It makes topology files. http://code.google.com/p/gmml/
> and http://code.google.com/p/gems/ are the development sites.
> The code there is still a bit new, but being used and tested
> regularly at dev.glycam.org.
Very nice. Using gems would be problematic for us since Chimera is
distributed on Unix, Windows, and Mac, and using gems would require us
to compile and distribute a Javascript interpreter for those
platforms. Urg. Also, I think using gmml would be significantly more
work than switching from sleap to tleap (even assuming gmml compiles
on all three platforms). A long term plan is to have Chimera "talk"
to Amber more directly by linking with SFF routines, so using gmml
could be considered as an alternative/complement.
I guess my plan for now is to stick with sleap and hope development on
it continues. If AmberTools13 rolls around and sleap development has
continued to lie fallow, I'll bite the bullet and switch to tleap (if
I still haven't gotten to the SFF/gmml stuff).
Thanks for the info!
--Eric
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Received on Fri May 18 2012 - 11:30:03 PDT
