NMR Restraints Grid

Result table
 (Save to zip file containing files for each block)

image	mrblock_id	pdb_id	bmrb_id	cing	stage	position	program	type
	567622	2mco	19448	cing	1-original	6	XPLOR/CNS	unknown

{====>} 
evaluate ($init_t = 2000)            {*Initial annealing temperature, in K.*}
{====>} 
evaluate ($cool_steps = 8000 )      {*Total number of steps during cooling.*}

parameter                                        {*Read the parameter file.*}
{====>} 
   @/home1/mike/tom/parallhdg.dna
end

parameter
   @/home1/mike/tom/tw3.par
end

{====>} structure @/home1/mike/tom/newcomplex_min_xpl.psf end                  {*The structure file.*}



noe
{====>}                                                        
   nres=2000             {*Estimate greater than the actual number of NOEs.*}
   class all 
{====>}
!ligdnarestraints below changed to previous file
   @/home1/mike/tom/ligdnarestraints5.txt  {*Read NOE distance ranges.*}
   @/home1/mike/tom/Hbonds.txt
end

!@../dihedral_ligand.tbl

                           {*Friction coefficient for MD heatbath, in 1/ps.*}
vector do (fbeta=10) (all)
vector do (mass=100) (all)      {*Heavy masses to speed molecular dynamics.*}

noe                             {*Parameters for NOE effective energy term.*}
   ceiling=1000                      
   averaging  * sum
   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

{---------------------------------------------------------------------------}

@/home1/mike/tom/tetradbaseplane.txt
end
@/home1/mike/tom/ligrestraints.txt

!end commented out (below)

end                      
{----------------------------------------------------------------------------}
 
set seed=27561 

end

{====>}
evaluate ($end_count=5)        {*Loop through a family of 5 structures.*}

evaluate ($count = 0)
while ($count < $end_count ) loop main 
    
   evaluate ($count=$count+1)
      
{====>}                             {*Filename(s) for embedded coordinates.*}
  { evaluate ($filename="gsba_"+encode($count)+".pdb")}
      
!next line altered to start with an already low E struct (apart from intermol NOEs)
!  coor @/home1/mike/tom/tw3g3complexmd20_1.pdb
   coor @/home1/mike/tom/otherisomer/changedtootherisomer1stcol.pdb

{----------------------------------------------------------------------------}
!   restraints harmonic exponent=2

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

   vector do (vx=maxwell($init_t)) ( all )
   vector do (vy=maxwell($init_t)) ( all )
   vector do (vz=maxwell($init_t)) ( all )

   evaluate ($final_t = 100)     { K }
   evaluate ($tempstep = 20)    { K }

   evaluate ($ncycle = ($init_t-$final_t)/$tempstep)
   evaluate ($nstep = int($cool_steps/$ncycle))

   evaluate ($ini_rad  = 0.75)        evaluate ($fin_rad  = 0.75)
   evaluate ($ini_con=  0.00000001)       evaluate ($fin_con=  4.0)

   evaluate ($bath  = $init_t)
   evaluate ($k_vdw = $ini_con)
   evaluate ($k_vdwfact = ($fin_con/$ini_con)^(1/$ncycle))
   evaluate ($radius=    $ini_rad)
   evaluate ($radfact = ($fin_rad/$ini_rad)^(1/$ncycle))

   evaluate ($i_cool = 0)

minimize powell nstep= 500 nprint=50 end
!removed 'end' here

   while ($i_cool < $ncycle) loop cool
      evaluate ($i_cool=$i_cool+1)

      evaluate ($bath  = $bath  - $tempstep)       
      evaluate ($k_vdw=min($fin_con,$k_vdw*$k_vdwfact))
      evaluate ($radius=max($fin_rad,$radius*$radfact))

      parameter  nbonds repel=$radius   end end 
      constraints interaction (all) (all) weights * 1. vdw $k_vdw end end
      constraints interaction (all) (all) weights * 1. end end

      dynamics  verlet
         nstep=$nstep time=0.0005 iasvel=current firstt=$bath 
         tcoup=true tbath=$bath nprint=$nstep iprfrq=0  
      end
 
{====>}                                                  {*Abort condition.*}
      evaluate ($critical=$temp/$bath) 
      if ($critical >  10. ) then
         display  ****&&&& rerun job with smaller timestep (i.e., 0.003) 
         stop
      end if
   end loop cool
      
   {* ================================================= Final minimization.*}
 
!  @/home1/mike/tom/tetradbaseplanerelaxed.txt
  @/home1/mike/tom/ligrestraints.txt
!  end
  minimize powell nstep= 500 nprint=50 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 ($filename="tw3g3complexmd10_"+encode($count)+".pdb")
      
   write coordinates output =$filename end
    
end loop main

stop

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