fix parameters in examples

examples/thirdparty/openmm/openmm-topoaa-flexref-test.cfg

@@ -50,11 +50,13 @@ reference_fname = "data/1nx1_refe.pdb"
 tolerance = 20
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle2 = 2
-fle_sta_2_1 = 1
-fle_end_2_1 = 5
-fle_sta_2_2 = 6
-fle_end_2_2 = 11
+nfle = 2
+fle_sta_1 = 1
+fle_end_1 = 5
+fle_seg_1 = "B"
+fle_sta_2 = 6
+fle_end_2 = 11
+fle_seg_2 = "B"
 # Define automatically dihedral restraints
 # for alpha and beta secondary structure elements
 ssdihed = "alphabeta"

src/haddock/modules/refinement/openmm/defaults.yaml

@@ -224,7 +224,9 @@ iniseed:
   max: 1000000
   title: Simulation seed.
   short: Set a pseudo-random seed for the simulation.
-  long: Set a pseudo-random seed for the simulation. This defines how the initial velocities are created, but has no effect on the randomicity of the solvation box.
+  long: Set a pseudo-random seed for the simulation. This defines how the
+    initial velocities are created, but has no effect on the randomicity
+    of the solvation box.
   group: 'sampling'
   explevel: easy
 
@@ -245,7 +247,8 @@ solv_equilibration:
   type: boolean
   title: Process the solvent equilibration phase.
   short: Process the solvent equilibration phase.
-  long: Process the solvent equilibration phase. If 'true', the solvent will be equilibrated while constraining proteins positions to intial ones.
+  long: Process the solvent equilibration phase. 
+    If 'true', the solvent will be equilibrated while constraining proteins positions to intial ones.
   group: 'sampling'
   explevel: easy