source leaprc.GLYCAM_06

####
####   1. Inversion at the anomeric center
#### 
  ###
  ### A minimial unit that causes trouble
  ###      Here, the 0GA is changed from alpha (axial) to beta (equatorial)
  ###
   m = sequence {OME}
   b = sequence {0GA}  
   set m tail m.1.O
   m = sequence {m b}
   saveamberparm m invert1.top invert1.rst
   savepdb m invert1.pdb
  ### The following, however, does not invert alpha to beta
   b = sequence {0GA}  
   saveamberparm b good1.top good1.rst
   savepdb b good1.pdb
  ###
  ### A variant of the minimial unit that does not invert
  ###
   m = sequence {OME}
   set m tail m.1.O
   m = sequence {m 0GA}
   saveamberparm m good2.top good2.rst
   savepdb m good2.pdb
  ###
  ### Another small unit that does not invert
  ###
   m = sequence {OME}
   set m tail m.1.O
   b = 0GA  
   m = sequence {m b}
   saveamberparm m good3.top good3.rst
   savepdb m good3.pdb
  ###
  ### A small context for the procedure that is inverting
  ###      ... as in this is why we might need/want to do that minimal thing
  ###      Here, the 3LB is changed from beta (equatorial) to alpha (axial)
  ###
   chain = sequence {OME VLB 0GA}
   branch = sequence {3LB 0MA}  ## inverts 3LB from beta to alpha
   set chain tail chain.2.O6
   molecule = sequence {chain branch}
   saveamberparm molecule invert2.top invert2.rst
   savepdb molecule invert2.pdb
  
####
####   2. Other build issues with copy
####     (sometimes anomeric inversion; not always; not here)
#### 
  ### This build is as expected
  ###
   n = 0SA
   n = sequence { OME n } 
   saveamberparm n copy-no.top copy-no.rst
   savepdb n copy-no.pdb
  ### We think this is also a chirality thing, just not 
  ###    at the anomeric center (this time).  
   p = copy 0SA
   p = sequence { OME p }
   saveamberparm p copy-yes.top copy-yes.rst
   savepdb p copy-yes.pdb

####
####   3. Impose problems
#### 
  ###
  ### Order matters -- note red-shift (blue shift?) in angles....
  ###
  m = sequence { OME 4GA 4GA 4GA 4GA 4GA 0GA }
  impose m {3 2} { {C2 C1 O4 C4 -40.0} }  ## builds as -50
  impose m {4 3} { {C2 C1 O4 C4 -50.0} }  ## builds as -60
  impose m {5 4} { {C2 C1 O4 C4 -60.0} }  ## builds as -70
  impose m {6 5} { {C2 C1 O4 C4 -70.0} }  ## builds as -80
  impose m {7 6} { {C2 C1 O4 C4 -80.0} }  ## builds as -80
  saveamberparm m imp_shift.top imp_shift.rst
  savepdb m imp_shift.pdb
  ###
  m = sequence { OME 4GA 4GA 4GA 4GA 4GA 0GA }
  impose m {7 6} { {C2 C1 O4 C4 -80.0} }  ## builds as -80
  impose m {6 5} { {C2 C1 O4 C4 -70.0} }  ## builds as -70
  impose m {5 4} { {C2 C1 O4 C4 -60.0} }  ## builds as -60
  impose m {4 3} { {C2 C1 O4 C4 -50.0} }  ## builds as -50
  impose m {3 2} { {C2 C1 O4 C4 -40.0} }  ## builds as -40
  saveamberparm m imp_ok.top imp_ok.rst
  savepdb m imp_ok.pdb

quit