Hi Ishima-san, I've attached a slightly modified version of your file to this email. I just changed the high temperature from 2000K to 3000K and the number of cooling steps from 3000 to 12000. It should work better, but let me know if it doesn't.
--JK Rieko Ishima wrote: > > Hi John > > I ran xplor using the protocol (with dipolar coupling) that you and Kirstin > worked for me. > Although the old dgsa protocol minimizes structures very well, the protocol > with dipolar coupling did not. I mean that b-sheets in rigid part are not > superimposed well (but folding is O.K.). I ran it without sani part, but > the results were almost the same. > > The data I used are noe, dihedral couplings (not so much), and N-Hn dipolar > couplings. Can you check again that the protocol is supposed to be enough > to minimize the structure even in such a data set? > > Thank you for your help. > > Rieko > > ------------------------------------------------------------------------ > > sa_dipo4.inpName: sa_dipo4.inp > Type: Plain Text (text/plain) > > ------------------------------------------------------------------------ > ---------------------------<>-------------------------------- > Rieko Ishima, Ph.D. > > Bldg 30, Rm 109, NIH, NIDCR, > 30 Convent Dr., Bethesda, MD 20892-4307, USA > e-mail: [email protected] > tel: 301-402-3160 (or 301-402-3149) > fax: 301-402-5321 (or 301-480-0240) -- Dr John Kuszewski 301-594-5831 (voice) 301-402-2867 (fax) [email protected] next part -------------- REMARKS This protocol allows computer to select dimer noes REMARKS very slow cooling with increase of vdw evaluate ($seed=65748309) set seed $seed end !---------------------------------------------------------------------- ! read in the PSF file and initial structure ! read in the PSF file and initial structure structure @all.psf @axis_500.psf end parameter {====>} ! @TOPPAR:parallhdg_procheck.pro ! the one with proline in seq. @TOPPARN:parallhdg_pc_new.pro @TOPPAR:parnah1er1_mod_new.inp @TOPPAR:par_axis_3.pro bond CP NH3 $kbon 1.473 ! CP - proline at N terminus angle CP CP NH3 $kang 103.2 ! CP - proline at N terminus angle HA CP NH3 $kang 109.5 ! CP - proline at N terminus angle CT NH3 CP $kang 112.0 ! CP - proline at N terminus improper HC HC CT CP 50.0 0 -70.0 ! N-term Pro improper HA HA CP NH3 $kchi 0 -70.874 ! CP methylene end coor @all.pdb !protein pdb + axis pdb !delete select (resid 1:2) end !delete select (resid 48:53) end !delete select (resid 85:95) end ! set the weights for the experimental energy terms evaluate ($knoe = 50.0) ! noes evaluate ($asym = 0.1) ! slope of NOE potential evaluate ($kcdi = 10.0) ! torsion angles evaluate ($kandb = 0.001) evaluate ($kimdb = 0.001) evaluate ($k_ncs = 0.01) !evaluate ($kprot = 0.1) !proton shifts !evaluate ($kprotd = 0.1) !proton shifts evaluate ($krama = 0.002) !rama evaluate ($kandb = 0.001) evaluate ($kimdb = 0.001) evaluate ($kramalr = 0.001) !long range rama evaluate ($kvirt1doverall=0.0001) evaluate ($kvirt1d=0.001) evaluate ($kvirt2d=0.001) evaluate ($kvirt3d=0.001) evaluate ($knuc = 0.001) !rama evaluate ($kdip = 1.0) !dipolar !--------------------------------------------------------------------------- ! Read experimental restraints !set message off echo off end noe nres = 16000 class all @hchcnoe.xplor @noesy15n.xplor @hbond.xplor end ! set echo on message on end noe ceiling 1000 averaging all sum potential all square scale all $knoe sqconstant all 1.0 sqexponent all 2 end !set message off echo off end set message on echo on end restraints dihed reset scale $kcdi nass = 5000 @angle.xplor end !set message on echo on end evaluate ($ksani = 0.01) evaluate ($ksani_CH = 1.0*$ksani) evaluate ($ksani_CACO = 0.035*$ksani) evaluate ($ksani_NCO = 0.050*$ksani) evaluate ($ksani_HNC = 0.108*$ksani) evaluate ($ksani_prot = 1.0*$ksani) evaluate ($ksani_dna = 0.25*$ksani) evaluate ($ksani_CH_dna = 1.0*$ksani) sani nres=1600 class JNH force $ksani potential harmonic coeff 0.0 5.817 0.326 @dip.xplor !dipolar coupling restraints end evaluate ($rcon = 0.003) parameters nbonds atom nbxmod 4 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=$rcon ! actually set the vdW weight end end rama nres=10000 !set message off echo off end @/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/shortrange_g aussians.tbl @/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/new_shortran ge_force.tbl @/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/all_na_gauss ians.tbl @/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/force_nuclei c.tbl end set message on echo on end @/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/newshortrang e_setup.tbl @/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/setup_nuclei c_new.tbl ! Fixing the axis using harmonic restraint ! leave out, let both rotate vector do (refx=x) (all) vector do (refy=y) (all) vector do (refz=z) (all) constraints fix (resid 500 and name OO) end evaluate ($cool_steps = 12000) evaluate ($init_t = 3000.01) vector do (mass = 100.0) (not resid 500 ) vector do (mass = 30.0) (resid 500 ) vector do (fbeta = 10.0) (all) ! coupling to heat bath coor copy end {* Generate Structures 1 -> 10 *} evaluate ($count =0) while ($count < 5) loop structure evaluate ($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_prot = 0.5) evaluate ($fin_prot = 7.5) evaluate ($ini_protd = 0.1) evaluate ($fin_protd = 1.5) evaluate ($ini_rad = 0.9) evaluate ($fin_rad = 0.78) evaluate ($ini_con= 0.004) evaluate ($fin_con= 4.0) evaluate ($ini_ang = 0.4) evaluate ($fin_ang = 1.0) evaluate ($ini_imp = 0.1) evaluate ($fin_imp = 1.0) evaluate ($ini_noe = 2.0) evaluate ($fin_noe = 30.0) evaluate ($knoe = $ini_noe) ! slope of NOE potential evaluate ($ini_rama = 0.002) evaluate ($fin_rama = 1.0) evaluate ($krama = $ini_rama) evaluate ($ini_lr = 0.0002) evaluate ($fin_lr = 0.15) evaluate ($kramalr = $ini_lr) evaluate ($ini_nuc = 1.000) evaluate ($fin_nuc = 2.0) evaluate ($knuc = $ini_nuc) evaluate ($virt1d=$kramalr) evaluate ($virt2d=$kramalr) evaluate ($virt3d=$kramalr) evaluate ($ini_andb = 0.001) evaluate ($fin_andb = 1000.0) evaluate ($kandb = $ini_andb) evaluate ($ini_imdb = 0.001) evaluate ($fin_imdb = 2000.0) evaluate ($kimdb = $ini_imdb) evaluate ($ini_kbb_a = 500.0) evaluate ($fin_kbb_a = 100.0) evaluate ($kbbang = $ini_kbb_a) evaluate ($ini_kbb_i = 500.0) evaluate ($fin_kbb_i = 10.0) evaluate ($kbbimp = $ini_kbb_i) evaluate ($kcdi = 10.0) ! torsion angles evaluate ($ini_sani = 0.01) evaluate ($fin_sani = 1.0) evaluate ($ksani = $ini_sani) ! !!evaluate ($ksani_CH = 1.0*$ksani) !!evaluate ($ksani_CACO = 0.035*$ksani) !!evaluate ($ksani_NCO = 0.050*$ksani) !!evaluate ($ksani_HNC = 0.108*$ksani) evaluate ($ksani_prot = 1.0*$ksani) !!evaluate ($ksani_CH_dna = 1.0*$ksani) !!sani class JNH force $ksani end !!sani class JCACO force $ksani_CACO end !!sani class JNCO force $ksani_NCO end !!sani class JCH force $ksani_CH end !!sani class JHNC force $ksani_HNC end sani class JNH force $ksani end !!sani class JCHd force $ksani_CH_dna end {evaluate ($kprot = $ini_prot) !proton shifts evaluate ($kprotd = $ini_protd) !proton shifts} flags exclude * include bonds angl impr vdw noe cdih rama sani end noe averaging all sum potential all square scale all $knoe sqconstant all 1.0 sqexponent all 2 end restraints dihed scale $kcdi end rama @/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/new_shortran ge_force.tbl !@/net/octave2/clore/xplor_40/gaussians/longrange_4D_hstgp_force.tbl !@/net/octave2/clore/xplor_40/gaussians/virtualTA_force_hstgp.tbl @/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/force_nuclei c.tbl end evaluate ($rcon = 1.0) parameters nbonds atom nbxmod 4 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 constraints interaction (not name ca) (all) weights * 1 angl 0.4 impr 0.1 vdw 0 elec 0 end interaction (name ca) (name ca) weights * 1 angl 0.4 impr 0.1 vdw 1.0 end end dynamics verlet nstep=5000 ! timestep=0.005 ! iasvel=maxwell firsttemp= $init_t tcoupling = true tbath = $init_t nprint=50 iprfrq=0 ntrfr = 99999999 end parameters nbonds atom nbxmod 4 wmin = 0.01 ! warning off cutnb = 4.5 ! nonbonded cutoff tolerance 0.5 repel= 0.9 ! scale factor for vdW radii = 1 ( L-J radii) rexp = 2 ! exponents in (r^irex - R0^irex)^rexp irex = 2 rcon =1.0 ! actually set the vdW weight end end evaluate ($kcdi = 200) restraints dihed scale $kcdi end evaluate ($final_t = 100) { K } evaluate ($tempstep = 25) { K } evaluate ($ncycle = ($init_t-$final_t)/$tempstep) evaluate ($nstep = int($cool_steps*4.0/$ncycle)) 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/$ncycle)) evaluate ($krama = $ini_rama) evaluate ($lr_fac = ($fin_lr/$ini_lr)^(1/$ncycle)) evaluate ($kramalr = $ini_lr) evaluate ($nuc_fac = ($fin_nuc/$ini_nuc)^(1/$ncycle)) evaluate ($knuc = $ini_nuc) evaluate ($virt1d=$kramalr) evaluate ($virt2d=$kramalr) evaluate ($virt3d=$kramalr) evaluate ($andb_fac = ($fin_andb/$ini_andb)^(1/$ncycle)) evaluate ($kandb = $ini_andb) evaluate ($imdb_fac = ($fin_imdb/$ini_imdb)^(1/$ncycle)) evaluate ($kimdb = $ini_imdb) evaluate ($kbb_fac_i = ($fin_kbb_i/$ini_kbb_i)^(1/$ncycle)) evaluate ($kbb_fac_a = ($fin_kbb_a/$ini_kbb_a)^(1/$ncycle)) evaluate ($kbbang = $ini_kbb_a) evaluate ($kbbimp = $ini_kbb_i) evaluate ($sani_fac = ($fin_sani/$ini_sani)^(1/$ncycle)) evaluate ($ksani = $ini_sani) !!evaluate ($ksani_CH = 1.0*$ksani) !!evaluate ($ksani_CACO = 0.035*$ksani) !!evaluate ($ksani_NCO = 0.050*$ksani) !!evaluate ($ksani_HNC = 0.108*$ksani) evaluate ($ksani_prot = 1.00*$ksani) evaluate ($ksani_CH_dna = 1.00*$ksani) flags exclude * include bonds angl impr vdw noe rama cdih sani end vector do (vx = maxwell($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 ($krama = $krama*$rama_fac) evaluate ($kramalr = $kramalr*$lr_fac) evaluate ($knuc = $knuc*$nuc_fac) evaluate ($virt1d=$kramalr) evaluate ($virt2d=$kramalr) evaluate ($virt3d=$kramalr) evaluate ($kandb = $kandb*$andb_fac) evaluate ($kimdb = $kimdb*$imdb_fac) evaluate ($kbbang = $kbbang*$kbb_fac_a) evaluate ($kbbimp = $kbbimp*$kbb_fac_i) evaluate ($ksani = $ksani*$sani_fac) !!evaluate ($ksani_CH = 1.0*$ksani) !!evaluate ($ksani_CACO = 0.035*$ksani) !!evaluate ($ksani_NCO = 0.050*$ksani) !!evaluate ($ksani_HNC = 0.108*$ksani) evaluate ($ksani_prot = 1.00*$ksani) !!evaluate ($ksani_dna = 0.25*$ksani) evaluate ($ksani_CH_dna = 1.00*$ksani) constraints interaction (all) (all) weights * 1 angles $k_ang improper $k_imp end end parameter nbonds cutnb=4.5 rcon=$k_vdw nbxmod=4 repel=$radius end end noe scale all $knoe end !! sani class JNH force $ksani end !! sani class JCACO force $ksani_CACO end !! sani class JNCO force $ksani_NCO end !! sani class JCH force $ksani_CH end !! sani class JHNC force $ksani_HNC end sani class JNH force $ksani end rama @/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/new_shortran ge_force.tbl !@/net/octave2/clore/xplor_40/gaussians/longrange_4D_hstgp_force.tbl !@/net/octave2/clore/xplor_40/gaussians/virtualTA_force_hstgp.tbl @/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/force_nuclei c.tbl end dynamics verlet nstep=$nstep timestep=0.005 iasvel=current firsttemp= $bath tcoupling = true tbath = $bath nprint=$nstep iprfrq=0 ntrfr = 99999999 end end loop cool mini powell nstep= 250 nprint= 50 end 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=0.5 class JNH end evaluate ($rms_sani_JNH=$result) evaluate ($viol_sani_JNH=$violations) remarks =============================================================== remarks overall,bonds,angles,improper,cidh,vdw, noe, rama, sani remarks energies: $ener, $bond, $angl, $impr, $cdih, $vdw, $noe, $rama, $sani remarks =============================================================== remarks bonds,angles,impropers,cdih,noe remarks $rms_bonds,$rms_angles,$rms_impropers,$rms_cdih,$rms_noe remarks =============================================================== remarks cdih end_coup end_coup_gly noe remarks violations : $violations_cdih $end_viols $end_viols_g $violations_noe remarks shifts: $viol_shift remarks =============================================================== remarks ================== remarks sani NH remarks RMS sani: $rms_sani_JNH remarks R-factor sani: $R_JNH remarks viol sani: $viol_sani_JNH remarks =============================================================== {====>} {*Name(s) of the family of final structures.*} evaluate ($file = "sa_dip4_" + encode($count) + ".sa") write coor output= $file end end loop structure stop
