I'm trying to make sure the AmberTools documentation examples work for sleap this time around and found these. Sorry I didn't find them before...
1] sleap doesn't allow in-line comments like tleap does. I love to comment my code, especially when sharing. It would be great if it were possible to do that though I admit this isn't critical. If not made consistent with tleap, the difference should at least be documented. For example, in tleap I can successfully do something like:
impose glycan {3 2} { {C1 O4 C4 H4 0.0} } # set psi between 4YB & 4YB
...but in sleap, this happens:
[gtkleap]$ impose glycan {3 2} { {C1 O4 C4 H4 0.0} } # set psi between 4YB & 4YB
Error: wrong number of arguments
2] tleap happily builds me a topology and coordinate set from the attached input (see also the output), but sleap gives the following:
[gtkleap]$ saveamberparm glycan glycan.top glycan.crd
Error: sparm type does not exist!
3] I have no clue what that last error message means (sleap doesn't know the parm type?). I checked the manual and the term 'sparm' doesn't appear. The programmer's guide mentions 'sparm', but only in the context of a declaration. I realize it might be a tough order to fill, but either making the error messages more descriptive or documenting them well would be very useful.
:-) Lachele
--
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
706-542-0263
lfoley.ccrc.uga.edu
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
- application/octet-stream attachment: tleap.out
- application/octet-stream attachment: sleap.out
Received on Wed Dec 09 2009 - 14:00:05 PST
