NMR Restraints Grid |
Result table
image | mrblock_id | pdb_id | bmrb_id | cing | stage | position | program | type | subtype |
519511 | 2ldt | 17682 | cing | 1-original | 3 | XPLOR/CNS | protocol | structure calculation |
evaluate ($end_count=1) ! set number of structures to be calculated evaluate ($seed=93869099) set seed $seed end {====>} {====>} parameter {*Read the parameter file.*} {====>} @parnah1er1_mod_new.inp @par_axis_3.pro end evaluate ($knoe = 0.1) evaluate ($kcdi = 10.0) evaluate ($kori = 0.002) evaluate ($knuc = 0.002) {====>} structure @h27_912-888_H2.psf @axis_new.psf end {*Read the structure file.*} coor @../xplor_stuff/912-888/912-888_calcs/"test27_1_912-888_calcs_xxx.pdb" flags exclude * include bonds angles impr end mini powell nstep=100 step=1.0 end coor copy end @plane_888.inp @rna_orient_888.setup noe {====>} nres=3000 {*Estimate greater than the actual number of NOEs.*} class all {====>} @noe_912-888_inter.tbl @noe_912-888_intra.tbl {*Read NOE distance ranges.*} class hb @hbond_912-888.tbl end {====>} restraints dihed scale $kcdi nass = 5000 set message on echo on end @912-888_chiral.tbl @aform_912-888.tbl @c2_912-888.tbl @c3_912-888.tbl @chi_912-888.tbl !dihedral angle restraints. set message on echo on end end noe {*Parameters for NOE effective energy term.*} ceiling=1000 averaging all sum potential all square sqconstant all 1. sqexponent all 2 scale all $knoe {*Constant NOE scale throughout the protocol.*} averaging hb sum potential hb biharmonic sqconstant hb 1. sqexponent hb 2 scale hb $knoe {*Constant NOE scale throughout the protocol.*} end evaluate ($knuc=0.1) rama nres=10000 set message off echo off end @nucleic_deltor_quarts2d.tbl @nucleic_deltor_quarts3d.tbl @nucleic_deltor_quarts4d.tbl @force_nucleic_quarts2d.tbl @force_nucleic_quarts3d.tbl @force_nucleic_quarts4d.tbl end set message on echo on end @setup_nucleic_2d3d.tbl @setup_nucleic_4d.tbl set message on echo on end evaluate ($ini_sani = 0.001) evaluate ($ksani = $ini_sani) sani nres=500 class JCHw ! allRDCs force $ksani potential harmonic coeff 0.0 -27.05 0.196 @dip_70_888_allRDCs.tbl class JCHf ! allRDCs force 0.0 !$ksani potential harmonic coeff 0.0 -27.05 0.196 @dip_30_888_allRDCs.tbl end parameter {*Parameters for the repulsive energy term.*} nbonds cutnb=6.5 rcon=4.0 nbxmod=3 repel=0.8 rexp=2 irex=2 wmin=0.01 tolerance=0.5 end end vector do (store1 = decode(resid)) (name C3') vector show min (store1) (name C3') evaluate ($first_residue = $result) vector show max (store1) (name C3') evaluate ($last_residue = $result) dynamics internal group (resid 500 ) hinge rotate (resid 500) evaluate ($res = 1) while ($res le 34) loop group group (resid $res and resname CYT and (name n1 or name c6 or name c5 or name c4 or name n3 or name c2)) group (resid $res and resname GUA and (name n9 or name c4 or name n3 or name c2 or name n1 or name c6 or name c5 or name n7 or name c8)) group (resid $res and resname ADE and (name n9 or name c4 or name n3 or name c2 or name n1 or name c6 or name c5 or name n7 or name c8)) group (resid $res and resname THY and (name n1 or name c6 or name c5 or name c4 or name n3 or name c2)) group (resid $res and resname URI and (name n1 or name c6 or name c5 or name c4 or name n3 or name c2)) evaluate ($res = $res +1) end loop group group (resid 34 and (name n1 or name c1 or name c2 or name o2 or name n3 or name c3 or name c4 or name n9 or name c8 or name n7 or name c5 or name c6 or name o6 or name h7)) set message on echo on end cloop=false auto torsion maxe 10000 end evaluate ($cool_steps = 3000) evaluate ($init_t = 2000.01) evaluate ($tol = $init_t/1000) vector do (mass = 100.0) (all) vector do (fbeta = 10.0) (all) {====>} evaluate ($count = 0) while ($count < $end_count ) loop structure evaluate ($count=$count+1) {====>} {*Filename(s) for embedded coordinates.*} vector do (x=xcomp) (all) vector do (y=ycomp) (all) vector do (z=zcomp) (all) evaluate ($ini_rad = 0.9) evaluate ($fin_rad = 0.78) evaluate ($ini_con= 0.004) evaluate ($fin_con= 4.0) evaluate ($rcon=$ini_con) evaluate ($ini_ang = 1.0) evaluate ($fin_ang = 1.0) evaluate ($ini_imp = 1.0) evaluate ($fin_imp = 1.0) evaluate ($ini_noe = 2.0) evaluate ($fin_noe = 30.0) evaluate ($knoe = $ini_noe) evaluate ($ini_nuc = 0.5) evaluate ($fin_nuc = 1.0) evaluate ($knuc = $ini_nuc) evaluate ($ini_orie = 0.002) evaluate ($fin_orie = 0.30) evaluate ($korie = $ini_orie) evaluate ($ini_sani = 0.01) evaluate ($fin_sani = 1.0) evaluate ($ksani = $ini_sani) evaluate ($kcdi = 10.0) ! torsion angles noe scale * $knoe end evaluate ($ksanib = $ksani) sani class JCHw force $ksani end restraints dihed scale $kcdi end rama @force_nucleic_quarts2d.tbl @force_nucleic_quarts3d.tbl @force_nucleic_quarts4d.tbl end orie scale $korie end evaluate ($rcon = 1.0) parameters nbonds atom nbxmod 3 wmin = 0.01 ! warning off cutnb = 100 ! nonbonded cutoff tolerance 45 repel= 1.2 ! scale factor for vdW radii = 1 ( L-J radii) rexp = 2 ! exponents in (r^irex - R0^irex)^rexp irex = 2 rcon=$rcon ! actually set the vdW weight end end flags exclude * include bond angl impr vdw noe cdih plan sani orie rama end !orie rama constraints interaction (not name c1' ) (all) weights * 1 angl 0.4 impr 0.1 vdw 0 elec 0 end interaction (name c1') (name c1') weights * 1 angl 0.4 impr 0.1 vdw 1.0 end end vector do (vx = maxwell($init_t)) (all) vector do (vy = maxwell($init_t)) (all) vector do (vz = maxwell($init_t)) (all) dynamics internal itype=pc6 !maxe=100 etol=$tol tbath=$init_t response= 20 response= 5 nstep=5000 timestep= 0.002 endtime=10 end parameters nbonds atom nbxmod 3 wmin = 0.01 ! warning off cutnb = 4.5 ! nonbonded cutoff tolerance 0.5 repel= 0.9 ! scale factor for vdW radii = 1 ( L-J radii) rexp = 2 ! exponents in (r^irex - R0^irex)^rexp irex = 2 rcon =1.0 ! actually set the vdW weight end end evaluate ($kcdi = 200) restraints dihed scale $kcdi end evaluate ($final_t = 25) { K } evaluate ($tempstep = 25) { K } evaluate ($ncycle = ($init_t-$final_t)/$tempstep) evaluate ($nstep = int($cool_steps*4.0/$ncycle)) evaluate ($endtime = $nstep*0.002) evaluate ($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/$ncycle)) evaluate ($k_ang = $ini_ang) evaluate ($ang_fac = ($fin_ang/$ini_ang)^(1/$ncycle)) evaluate ($k_imp = $ini_imp) evaluate ($imp_fac = ($fin_imp/$ini_imp)^(1/$ncycle)) evaluate ($noe_fac = ($fin_noe/$ini_noe)^(1/$ncycle)) evaluate ($knoe = $ini_noe) !evaluate ($rama_fac = ($fin_rama/$ini_rama)^(1/$ncycle)) evaluate ($nuc_fac = ($fin_nuc/$ini_nuc)^(1/$ncycle)) evaluate ($knuc = $ini_nuc) evaluate ($orie_fac = ($fin_orie/$ini_orie)^(1/$ncycle)) evaluate ($korie = $ini_orie) evaluate ($sani_fac = ($fin_sani/$ini_sani)^(1/$ncycle)) evaluate ($ksani = $ini_sani) evaluate ($ksanib = $ksani) evaluate ($ksanin = $ksani*1.0) evaluate ($ksanim = $ksani*1.0) evaluate ($ksaddr = $ksani*1/5) evaluate ($ksaddb = $ksani*1/8) sani class JCHw force $ksani end flags exclude * include bond angl impr vdw noe cdih plan sani orie rama end vector do (vx = maxwell($bath)) (all) vector do (vy = maxwell($bath)) (all) vector do (vz = maxwell($bath)) (all) 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*$radfact)) evaluate ($k_ang = $k_ang*$ang_fac) evaluate ($k_imp = $k_imp*$imp_fac) evaluate ($knoe = $knoe*$noe_fac) evaluate ($knuc = $knuc*$nuc_fac) evaluate ($korie = $korie*$orie_fac) evaluate ($ksani = $ksani*$sani_fac) evaluate ($ksanib = $ksani) evaluate ($ksanin = $ksani*1.0) evaluate ($ksanim = $ksani*1.0) evaluate ($ksaddr = $ksani*1/5) evaluate ($ksaddb = $ksani*1/8) sani class JCHw force $ksani end constraints interaction (all) (all) weights * 1 angles $k_ang improper $k_imp end end parameter nbonds cutnb=4.5 rcon=$k_vdw nbxmod=3 repel=$radius end end noe scale * $knoe end rama @force_nucleic_quarts2d.tbl @force_nucleic_quarts3d.tbl @force_nucleic_quarts4d.tbl end orie scale $korie end dynamics internal itype=pc6 !maxe=100 etol=$tol tbath=$bath response= 20 response= 5 nstep=$nstep endtime=$endtime timestep= 0.002 end end loop cool dynamics internal itype=powell nstep=200 maxcalls=20000 nprint=1 etol=1e-7 gtol=0.01 depred=0.001 end {* =================================== Write out the final structure(s).*} print threshold=0.5 noe evaluate ($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=$result) sani print threshold=5.0 class JCHw end evaluate ($rms_JCHw=$result) evaluate ($R_JCHw=$result*100/23.86) sani print threshold=5.0 class JCHf end evaluate ($rms_JCHf=$result) evaluate ($R_JCHf=$result*100/23.86) remarks =============================================================== remarks overall,bonds,angles,improper,vdw,noe,cdih,rama,orie,plan,sani,orie remarks energies: $ener, $bond, $angl, $impr, $vdw, $noe, $cdih, $plan, $sani, $orie 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 =============================================================== remarks R-factor: JCH_work (70%) JCH_free (30%) remarks R-factor sani: $R_JCHw $R_JCHf remarks rms sani: $rms_JCHw $rms_JCHf remarks =============================================================== {====>} {*Name(s) of the family of final structures.*} evaluate ($filename="test27_xxx_allRDCs.sa") write coordinates output =$filename end end loop structure stop
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