The following script for CNS simulated annealing was submitted by trent. He recommends to use this script as a part of RECOORD structure determination and water refinement protocol to prevent wrong geometry of aromatic rings (as reported here and here). You may find this script useful if you have a ligand in your model that makes CNS go crazy and produce protein structures with collapsed aromatic rings.
Thanks trent! Mark ************************************************** ***************** remarks file sa_cns.inp remarks Simulated annealing protocol for NMR structure determination with cns. remarks The starting structure for this protocol can be any structure with remarks a reasonable geometry, such as randomly assigned torsion angles or remarks extended strands. remarks based on sa_new.inp from xplor remarks high_steps and cool_steps increased 4 fold to improve convergence remarks uses parallhdg5.3.pro and topallhdg5.3.pro from recoord without error remarks works with additional ligand files remarks Author: Trent Bjorndahl {====>} evaluate ($init_t = 1000 ) {====>} evaluate ($high_steps= 24000 ) {====>} evaluate ($cool_steps = 12000 ) parameter {====>} @parallhdg5.3.pro !@yourparameterfilehere.par end {====>} structure @yourstructurefile.mtf end {*Read the structure file.*} {====>} coordinates @yourcoordinatefile.pdb {*Read the coordinates.*} noe {====>} nres=10000 {*Estimate greater than the actual number of NOEs.*} class all {====>} @noes.tbl {*Read NOE distance ranges.*} end {====>} restraints dihedral reset nass = 1000 @dihedrals.tbl end flags exclude * include bonds angle impr vdw noe cdih end {*Friction coefficient for MD heatbath, in 1/ps. *} do (fbeta=10) (all) {*Uniform heavy masses to speed molecular dynamics.*} do (mass=100) (all) noe {*Parameters for NOE effective energy term.*} ceiling=1000 averaging * cent potential * soft scale * 50. sqoffset * 0.0 sqconstant * 1.0 sqexponent * 2 soexponent * 1 asymptote * 0.1 {*Initial value--modified later.*} rswitch * 0.5 end parameter {*Parameters for the repulsive energy term.*} nbonds repel=1. {*Initial value for repel--modified later.*} rexp=2 irexp=2 rcon=1. nbxmod=3 wmin=0.01 cutnb=4.5 ctonnb=2.99 ctofnb=3. tolerance=0.5 end end restraints dihedral scale=5. end {====>} evaluate ($end_count=10) {*Loop through a family of 10 structures.*} coor copy end evaluate ($count = 0) while ($count < $end_count ) loop main evaluate ($count=$count+1) coor swap end coor copy end {* Initial minimization.*} restraints dihedral scale=5. end noe asymptote * 0.1 end parameter nbonds repel=1. end end igroup interaction (all) (all) weights * 1 vdw 0.002 end end minimize powell nstep=50 drop=10. nprint=25 end {* High-temperature dynamics.*} igroup interaction (all) (all) weights * 1 angl 0.4 impr 0.1 vdw 0.002 end end evaluate ($nstep1=int($high_steps * 2. / 3. ) ) evaluate ($nstep2=int($high_steps * 1. / 3. ) ) dynamics cartesian nstep=$nstep1 timestep=0.003 temperature=$init_t tcoup=true nprint=50 ntrfrq=9999 cmremove=true cmperiodic=0 end {* Tilt the asymptote and increase weights on geometry.*} noe asymptote * 1.0 end igroup interaction (all) (all) weights * 1 vdw 0.002 end end {* Bring scaling factor for S-S bonds back *} parameter bonds ( name SG ) ( name SG ) 1000. TOKEN angle ( name CB ) ( name SG ) ( name SG ) 500. TOKEN end dynamics cartesian nstep=$nstep2 timestep=0.003 tcoup=true temperature=$init_t nprint=50 ntrfrq=9999 cmremove=true cmperiodic=0 end {* Cool the system.*} restraints dihedral scale=200. end evaluate ($final_t = 100) { K } evaluate ($tempstep = 50) { K } evaluate ($ncycle = ($init_t-$final_t)/$tempstep) evaluate ($nstep = int($cool_steps/$ncycle)) evaluate ($ini_rad = 0.9) evaluate ($fin_rad = 0.75) evaluate ($ini_con= 0.003) evaluate ($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) 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 igroup interaction (all) (all) weights * 1. vdw $k_vdw end end dynamics cartesian nstep=$nstep time=0.005 tcoup=true temperature=$bath nprint=$nstep ntrfrq=9999 cmremove=true cmperiodic=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.*} igroup interaction (all) (all) weights * 1. vdw 1. end end parameter nbonds repel=0.80 rexp=2 irexp=2 rcon=1. nbxmod=3 wmin=0.01 cutnb=6.0 ctonnb=2.99 ctofnb=3. tolerance=1.5 end end minimize powell nstep=1000 drop=10.0 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,$rm s_cdih remarks ================================================== ============= remarks noe, cdih remarks violations.: $violations_noe, $violations_cdih remarks ================================================== ============= {====>} {*Name(s) of the family of final structures.*} evaluate ($filename="sa_cns_"+encode($count)+".pdb") write coordinates output =$filename end end loop main stop |
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