remarks file nmr/refine_gentle.inp  -- Gentle simulated annealing refinement 
remarks                                for NMR structure determination
remarks Author: Axel T. Brunger

{====>}
evaluate ($init_t = 300)                            {*SA temperature, in K.*}
{====>}
evaluate ($cool_steps = 20000 )                 {*Total number of SA steps.*}


parameter                                        {*Read the parameter file.*}
{====>} 
   @TOPPAR:parallhdg.dna
end

{====>} structure @generatedna.psf end           {*Read the structure file.*}

noe
{====>}                                                        
   nres=3000             {*Estimate greater than the actual number of NOEs.*}
   class all 
{====>}
   @inter2.tbl                                  {*Read NOE distance ranges.*}
   @intra2.tbl
   @hbonds.tbl
end

{====>}
@dihed.tbl                                {*Read dihedral angle restraints.*}


noe                             {*Parameters for NOE effective energy term.*}
   ceiling=1000                      
   averaging  * cent
   potential  * square
   sqconstant * 1.
   sqexponent * 2
   scale      * 50.           {*Constant NOE scale throughout the protocol.*}
end

parameter                       {*Parameters for the repulsive energy term.*}
   nbonds
      tolerance=0.5 
      cutnb=11.5 ctonnb=9.5 ctofnb=10.5 tolerance=0.5 rdie vswitch switch
   end
end

restraints dihedral 
        scale=200.         
end 

{====>}
evaluate ($end_count=2)            {*Loop through a family of 2 structures.*}

evaluate ($count = 0)
while ($count < $end_count ) loop main 
    
   evaluate ($count=$count+1)
      
{====>}                             {*Filename(s) for embedded coordinates.*}
   evaluate ($filename="dna_init_"+encode($count)+".pdb")
      
   coor @@$filename

   flags exclude * include bond angl impr vdw noe cdih elec dihe end


   {* ================================================ Intial minimization.*}
   minimize powell nstep= 200 nprint=25 end

   {* ============================================ Constant temperature SA.*}
   vector do ( fbeta=100. ) ( all )              {* Coupling to heat bath. *}
   dynamics  verlet                     
      nstep=$cool_steps timestep=0.001   
      iasvel=maxwell  firsttemperature=$init_t  
      tbath=300 
      nprint=250 iprfrq=2500 
      trajectory=refine_gentle.tra   nsavc=200 {* Save trajectory to file. *}
   end
   close refine_gentle.tra end

   {* ========================= Compute dynamics average over last 10 psec.*}   
   dynamics analysis average
       input=refine_gentle.tra begin=10000 skip=200 stop=$cool_steps
   end
   close refine_gentle.tra end
        
   {* ================================================= Final minimization.*}
   minimize powell nstep= 200 nprint=25 end
       
   {* =================================== Write out the final structure(s).*}
   print threshold=0.5 noe 
   evaluate ($rms_noe=$result)
   evaluate ($violations_noe=$violations)
   print threshold=5. cdih
   evaluate ($rms_cdih=$result)
   evaluate ($violations_cdih=$violations)
   print thres=0.05 bonds          
   evaluate ($rms_bonds=$result)
   print thres=5. angles
   evaluate ($rms_angles=$result)
   print thres=5. impropers
   evaluate ($rms_impropers=$result)
   remarks =============================================================== 
   remarks            overall,bonds,angles,improper,vdw,noe,cdih
   remarks energies: $ener, $bond, $angl, $impr, $vdw, $noe, $cdih 
   remarks =============================================================== 
   remarks            bonds,angles,impropers,noe,cdih
   remarks rms-d: $rms_bonds,$rms_angles,$rms_impropers,$rms_noe,$rms_cdih
   remarks =============================================================== 
   remarks               noe,  cdih
   remarks violations.: $violations_noe, $violations_cdih
   remarks =============================================================== 
      
{====>}                        {*Name(s) of the family of final structures.*}
   evaluate ($filename="refine_gentle_"+encode($count)+".pdb")
      
   write coordinates output =$filename end
    
end loop main

stop