remarks  file  xtalrefine/alternate.inp
remarks  Make alternate conformations 

                              {* Read parameter and topology files as usual.*}

 segment                                    

   name="LY  "                              

   chain
     @TOPPAR:toph19.pep                    

              {* Coordinate file contains only one conformer with LY segid. *}
     coordinates @LY.PDB end                 
   end                                       
 end

                                               {* Rename atoms if required. *} 
 vector do (name="O") ( name OT1 )               
 vector do (name="OT") ( name OT2 )
 vector do (name="CD1") ( name CD and resname ile )

                             {* Here we establish the alternate conformers. *}
 vector do (segid="LY-1") (resid 621 and not 
           (name ca or name c or name n or name o or name cb or name h )) 

 duplicate select=( segid "LY-1" ) segid="LY-2" end

                                  {* Here we actually read the coordinates. *}
                  {* Note different file from that read to obtain sequence. *}
 coordinates @LY-ALL.PDB end

    {* Now notify program that the alternate conformers can interact with   *}
    {* themselves or the rest of the protein, but not each other.           *}
    {* This information needed in other procedures, eg slowcool.inp as well.*}
 constraints
   inter = (segid = "LY  ") (segid = "LY  ")
   inter = (segid = "LY  " or segid = "LY-1") (segid = "LY-1")
   inter = (segid = "LY  " or segid = "LY-2") (segid = "LY-2")
 end

      {* Perform hydrogen building as usual.  Write molecular structure and *}
      {* coordinate file.                                                   *}