random.inp
Description: Binary data
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\f0\fs24 \cf0 X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR>X-PLOR> EVALUATE: symbol $INIT_T set to 1000.00 (real)\
X-PLOR> EVALUATE: symbol $TOL set to 1.00000 (real)\
X-PLOR>X-PLOR>PARRDR>PARRDR> ASSFIL: file /usr/share/xplor-nih-2.18/toppar/dnarnapar.cornish opened.\
PARRDR>remark file dnarnapar.cornish \
PARRDR>remark geometric energy function parameters for distance geometry and \
PARRDR>remark simulated annealing. \
PARRDR>remark \
PARRDR>remark history: 05/30/01 \
PARRDR>remark \
PARRDR>remark derived from parallhdg.dna \
PARRDR>remark \
PARRDR> \
PARRDR> \
PARRDR>set echo off end \
EVALUATE: symbol $KBOND set to 1000.00 (real)\
EVALUATE: symbol $KANGLE set to 500.000 (real)\
EVALUATE: symbol $KIMPROPER set to 500.000 (real)\
PARRDR>end \
X-PLOR> \
X-PLOR>\{====>\} \
X-PLOR>structure @sl2.psf end \{*Read the structure file.*\} \
ASSFIL: file /home/giedroc/structure_dg/sl2.psf opened.\
STRUcture>PSF \
REMARKS FILENAME="sl2.psf"\
REMARKS file dnarnapar.cornish\
REMARKS geometric energy function parameters for distance geometry and\
REMARKS simulated annealing.\
REMARKS\
REMARKS history: 05/30/01\
REMARKS\
REMARKS derived from parallhdg.dna\
REMARKS\
REMARKS DATE:11-Jul-06 10:14:07 created by user: [unknown]\
XPLOR: current counts (number in parenthesis is maximum)\
NATOM= 506(MAXA= 800) NBOND= 544(MAXB= 800)\
NTHETA= 973(MAXT= 1600) NGRP= 163(MAXGRP= 200)\
NPHI= 460(MAXP= 800) NIMPHI= 328(MAXIMP= 400) \
NDON= 47(MAXPAD= 200) NACC= 133(MAXPAD= 200)\
NNB= 48(MAXNB= 100) \
STRUcture> end \{*Read the structure file.*\} \
X-PLOR> \
X-PLOR>noe \
NOE>\{====>\} \
NOE> nres=3000 \{*Estimate greater than the actual number of NOEs.*\} \
NOE: allocating space for 3000 restraints.\
NOE> class all \
NOE>\{====>\} \
NOE> @030206_noe_all_rev.tbl \
ASSFIL: file /home/giedroc/structure_dg/030206_noe_all_rev.tbl opened.\
NOE>assign (residue 42 and name H1') (residue 42 and name H8) 4.0 1.0 1.0 \
SELRPN: 1 atoms have been selected out of 506\
SELRPN: 1 atoms have been selected out of 506\
\
ETC. (noes and h-bonding constraints read in fine)\
\
X-PLOR>\{====>\} evaluate ($end_count=100) \{* Number of structures. *\} \
X-PLOR> \
X-PLOR>evaluate ($count = 0) \
X-PLOR>while ($count < $end_count ) loop main \
X-PLOR> evaluate ($count=$count+1) \
X-PLOR> \
X-PLOR> \{* Generate a starting structure. *\} \
X-PLOR> vector do (x = (random()-0.5)*20) (all) \
X-PLOR> vector do (y = (random()-0.5)*20) (all) \
X-PLOR> vector do (z = (random()-0.5)*20) (all) \
X-PLOR> \
X-PLOR> vector do (fbeta=10) (all) \{*Friction coefficient for MD heatbath.*\} \
X-PLOR> vector do (mass=100) (all) \{*Uniform heavy masses to speed*\} \
X-PLOR> \{*molecular dynamics. *\} \
X-PLOR> \
X-PLOR> parameter nbonds \
NBDSET> atom cutnb 100 tolerance 45 repel=1.2 \
NBDSET> rexp=2 irexp=2 rcon=1.0 nbxmod 4 \
NBDSET> end end \
X-PLOR> \
X-PLOR> flags exclude * include bonds angle impr vdw noe cdih harm end \
X-PLOR> \
X-PLOR> evaluate ($knoe = 0.5) \
X-PLOR> \
X-PLOR> evaluate ($kbon = 0.00005 ) \{* Bonds. *\} \
X-PLOR> evaluate ($kang = 0.00005 ) \{* Angles. *\} \
X-PLOR> evaluate ($kimp = 0.0 ) \{* Impropers. *\} \
X-PLOR> evaluate ($kvdw = 0.1) \{* Vdw. *\} \
X-PLOR> constraints \
CONS> interaction (not name ca) (all) \
CONS> weights bond $kbon angl $kang impr $kimp vdw 0 elec 0 end \
CONS> interaction (name ca) (name ca) \
CONS> weights bond $kbon angl $kang impr $kimp vdw $kvdw end \
CONS> end \
X-PLOR> \
X-PLOR> \
X-PLOR> \{* ======================================== High temperature dynamics. *\} \
X-PLOR> \
X-PLOR> vector do (vx = maxwell($init_t)) (all) \
X-PLOR> vector do (vy = maxwell($init_t)) (all) \
X-PLOR> vector do (vz = maxwell($init_t)) (all) \
X-PLOR> \
X-PLOR> evaluate ($timestep = 0.04) \
X-PLOR> evaluate ($nstep = 100) \
X-PLOR> evaluate ($endtime = $nstep*.002) \
X-PLOR> \
X-PLOR> while ($kbon < 0.01) loop stage1 \
X-PLOR> \
X-PLOR> evaluate ($kbon = min(0.25, $kbon * 1.25)) \
X-PLOR> evaluate ($kang = $kbon) \
X-PLOR> evaluate ($kimp = 0) \
X-PLOR> \
X-PLOR> noe scale * $knoe end \
X-PLOR> restraints dihed scale 0. end \
X-PLOR> constraints \
CONS> interaction (not name ca) (all) \
CONS> weights bond $kbon angl $kang impr $kimp vdw 0 elec 0 end \
CONS> interaction (name ca) (name ca) \
CONS> weights bond $kbon angl $kang impr $kimp vdw $kvdw end \
CONS> end \
X-PLOR> \
X-PLOR>! dynamics verlet \
X-PLOR>! nstep=$nstep timestep=$timestep iasvel=current \
X-PLOR>! tcoupling=true tbath=$init_t nprint=50 iprfrq=0 \
X-PLOR>! end \
X-PLOR> \
X-PLOR> dynamics internal \
Internal Dynamics>! itype=pc6 \
Internal Dynamics> itype=verlet \
Internal Dynamics> etol=$tol \
Internal Dynamics> tbath=$init_t \
Internal Dynamics> response=20 \
Internal Dynamics> response=5 \
Internal Dynamics> nstep=$nstep \
Internal Dynamics> endtime=$endtime \
Internal Dynamics> timestep=$timestep \
Internal Dynamics> end \
AT_Build::buildNode: cycle link found between atoms 22 GUA 42 C5 and 12 GUA 42 C4 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 24 GUA 42 C8 and 11 GUA 42 N9 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 30 GUA 42 C3' and 6 GUA 42 C4' \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 55 ADE 43 C5 and 46 ADE 43 C4 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 57 ADE 43 C8 and 45 ADE 43 N9 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 63 ADE 43 C3' and 40 ADE 43 C4' \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 79 URI 44 C6 and 78 URI 44 N1 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 93 URI 44 C3' and 73 URI 44 C4' \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 109 CYT 45 C6 and 108 CYT 45 N1 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 124 CYT 45 C3' and 103 CYT 45 C4' \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 140 URI 46 C6 and 139 URI 46 N1 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 154 URI 46 C3' and 134 URI 46 C4' \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 170 CYT 47 C6 and 169 CYT 47 N1 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 185 CYT 47 C3' and 164 CYT 47 C4' \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 201 URI 48 C6 and 200 URI 48 N1 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 215 URI 48 C3' and 195 URI 48 C4' \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 231 URI 49 C6 and 230 URI 49 N1 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 245 URI 49 C3' and 225 URI 49 C4' \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 271 GUA 50 C5 and 261 GUA 50 C4 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 273 GUA 50 C8 and 260 GUA 50 N9 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 279 GUA 50 C3' and 255 GUA 50 C4' \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 295 URI 51 C6 and 294 URI 51 N1 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 309 URI 51 C3' and 289 URI 51 C4' \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 334 ADE 52 C5 and 325 ADE 52 C4 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 336 ADE 52 C8 and 324 ADE 52 N9 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 342 ADE 52 C3' and 319 ADE 52 C4' \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 368 GUA 53 C5 and 358 GUA 53 C4 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 370 GUA 53 C8 and 357 GUA 53 N9 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 376 GUA 53 C3' and 352 GUA 53 C4' \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 401 ADE 54 C5 and 392 ADE 54 C4 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 403 ADE 54 C8 and 391 ADE 54 N9 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 409 ADE 54 C3' and 386 ADE 54 C4' \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 425 URI 55 C6 and 424 URI 55 N1 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 439 URI 55 C3' and 419 URI 55 C4' \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 455 CYT 56 C6 and 454 CYT 56 N1 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 470 CYT 56 C3' and 449 CYT 56 C4' \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 495 ADE 57 C5 and 486 ADE 57 C4 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 497 ADE 57 C8 and 485 ADE 57 N9 \
removing bond.\
AT_Build::buildNode: cycle link found between atoms 503 ADE 57 C3' and 480 ADE 57 C4' \
removing bond.\
-- VERLET ------ step= 0 --- timestep= 0.04 --- energy evals= 1 --\
| E(kin)+E(poten)=25756.96 E(kin)=1510.462 temperature=1001.448 |\
| Etotal =24246.495 grad(E)=15.435 E(BOND)=5622.961 E(ANGL)=37.131 |\
| E(IMPR)=0.000 E(VDW )=0.000 E(HARM)=0.000 E(CDIH)=0.000 |\
| E(NOE )=18586.403 |\
-------------------------------------------------------------------------------\
-- VERLET ------ step= 1 --- timestep= 0.04 --- energy evals= 1 --\
| E(kin)+E(poten)=25756.96 E(kin)=1510.462 temperature=1001.448 |\
| Etotal =24246.495 grad(E)=15.435 E(BOND)=5622.961 E(ANGL)=37.131 |\
| E(IMPR)=0.000 E(VDW )=0.000 E(HARM)=0.000 E(CDIH)=0.000 |\
| E(NOE )=18586.403 |\
-------------------------------------------------------------------------------\
-- VERLET ------ step= 2 --- timestep= 0.04 --- energy evals= 1 --\
| E(kin)+E(poten)=26217.44 E(kin)=4353.501 temperature=2886.405 |\
| Etotal =21863.943 grad(E)=14.153 E(BOND)=5550.841 E(ANGL)=37.150 |\
| E(IMPR)=0.000 E(VDW )=0.000 E(HARM)=0.000 E(CDIH)=0.000 |\
| E(NOE )=16275.952 |\
-------------------------------------------------------------------------------\
-- VERLET ------ step= 3 --- timestep= 0.04 --- energy evals= 1 --\
| E(kin)+E(poten)=26308.83 E(kin)=8340.118 temperature=5529.563 |\
| Etotal =17968.716 grad(E)=11.881 E(BOND)=5417.063 E(ANGL)=37.256 |\
| E(IMPR)=0.000 E(VDW )=0.000 E(HARM)=0.000 E(CDIH)=0.000 |\
| E(NOE )=12514.397 |\
-------------------------------------------------------------------------------\
-- VERLET ------ step= 4 --- timestep= 0.04 --- energy evals= 1 --\
| E(kin)+E(poten)=26237.32 E(kin)=12511.2 temperature=8295.019 |\
| Etotal =13726.125 grad(E)=9.041 E(BOND)=5238.013 E(ANGL)=37.433 |\
| E(IMPR)=0.000 E(VDW )=0.000 E(HARM)=0.000 E(CDIH)=0.000 |\
| E(NOE )=8450.678 |\
-------------------------------------------------------------------------------\
-- VERLET ------ step= 5 --- timestep= 0.04 --- energy evals= 1 --\
| E(kin)+E(poten)=25870.47 E(kin)=15671.3 temperature=10390.19 |\
| Etotal =10199.176 grad(E)=6.310 E(BOND)=5031.144 E(ANGL)=37.692 |\
| E(IMPR)=0.000 E(VDW )=0.000 E(HARM)=0.000 E(CDIH)=0.000 |\
| E(NOE )=5130.339 |\
-------------------------------------------------------------------------------\
X-PLOR> \
X-PLOR> end loop stage1 \
X-PLOR> while ($kbon < 0.01) loop stage1 \
X-PLOR> \
X-PLOR> evaluate ($kbon = min(0.25, $kbon * 1.25)) \
X-PLOR> evaluate ($kang = $kbon) \
X-PLOR> evaluate ($kimp = 0) \
X-PLOR> \
X-PLOR> noe scale * $knoe end \
X-PLOR> restraints dihed scale 0. end \
X-PLOR> constraints \
CONS> interaction (not name ca) (all) \
CONS> weights bond $kbon angl $kang impr $kimp vdw 0 elec 0 end \
CONS> interaction (name ca) (name ca) \
CONS> weights bond $kbon angl $kang impr $kimp vdw $kvdw end \
CONS> end \
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