Show I put the upper/lower restraints in one file, for instance:
# Upper distance limit
29 VAL HA 29 VAL HB 5.94
29 VAL HA 29 VAL QG2 5.51
17 ILE QD1 17 ILE HB 5.61
# Lower distance limit
29 VAL HA 29 VAL HB 3.961
29 VAL HA 29 VAL QG2 3.673
17 ILE QD1 17 ILE HB 3.743
or put them separately in two files, one for upper limit and the other one for lower limit?
A) Rosetta in general does not use that format for constraints; see here: http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/co...
You will need to choose functional forms for the constraint. If you want a zero-potential basin, use bounded func.
B) This advice may not apply to some of the specific executeables that use nonstandard constraint formats (enzyme design comes to mind.)
C) You can put all your constraints in one file.