XPLOR-NIH version 2.18-pre4 C.D. Schwieters, J.J. Kuszewski, Progr. NMR Spectr. 48, 47-62 (2006). N. Tjandra, and G.M. Clore J. Magn. Res., 160, 66-74 (2003). http://nmr.cit.nih.gov/xplor-nih based on X-PLOR 3.851 by A.T. Brunger User: schwitrs on: tan (x86_64/Linux ) at: 11-Jun-07 15:21:40 X-PLOR>remarks DYNIOTEST.INP X-PLOR>remarks TEST DYNAMICS I/O AND MERGING X-PLOR>remarks by Axel Brunger, Cambridge, 6-OCT-83 X-PLOR>remarks ==================================== X-PLOR> X-PLOR>rtf @TOPPAR:toph11.pro end ASSFIL: file /home/schwitrs/xplor/toppar/toph11.pro opened. RTFRDR>REMARKS TOPH11.PRO ( from TOPH10.INP) RTFRDR>REMARKS ============================= RTFRDR>REMARKS Charges and atom order modified for neutral GROUPs. RTFRDR>REMARKS Histidine charges set to Del Bene and Cohen sto-3g calculations. RTFRDR>REMARKS Amide charges set to match the experimental dipole moment. RTFRDR>REMARKS DNA/RNA atoms appended . RTFRDR>REMARKS few atoms never referenced switched off. RTFRDR>REMARKS Default for HIStidines is the doubly protonated state RTFRDR> RTFRDR>set echo=false end RTFRDR> end X-PLOR>parameter @TOPPAR:param11.pro end ASSFIL: file /home/schwitrs/xplor/toppar/param11.pro opened. PARRDR>REMARKS PARAM11.PRO ( from PARAM6A ) PARRDR>REMARKS =========== PARRDR>REMARKS PROTEIN PARAMETERS: PARRDR>REMARKS PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) PARRDR>REMARKS TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) PARRDR>REMARKS LENNARD-JONES NONBONDED PARAMETERS WITH SPECIAL TREATMENT OF 1:4 PARRDR>REMARKS CARBON-CARBON INTERACTIONS: JORGENSON ET. AL. PARRDR>REMARKS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 PARRDR>REMARKS PARRDR>set echo=false end PARRDR> end X-PLOR> X-PLOR>segment SEGMENT> name=tryp SEGMENT> setup=true SEGMENT> chain CHAIN> @TOPPAR:toph11.pep ASSFIL: file /home/schwitrs/xplor/toppar/toph11.pep opened. CHAIN>REMARKS TOPH11-MACRO for protein sequence CHAIN>SET ECHO=FALSE END CHAIN> sequence SEQUENCE> TRP MAPIC: Atom numbers being modified SEQUence-element (terminate with END) = end MAPIC: Atom numbers being modified CHAIN> end SEGMENT>end SEGMNT: 1 residues were inserted into segment "TRYP" XPLOR: current counts (number in parenthesis is maximum) NATOM= 19(MAXA= 200) NBOND= 20(MAXB= 100) NTHETA= 28(MAXT= 100) NGRP= 6(MAXGRP= 100) NPHI= 10(MAXP= 100) NIMPHI= 15(MAXIMP= 100) NDON= 4(MAXPAD= 100) NACC= 2(MAXPAD= 100) NNB= 36(MAXNB= 100) X-PLOR> X-PLOR>coor COOR> remarks TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, COOR> remarks AND CG 50 STEPS COOR> remarks EPS=R POTENTIAL COOR> natoms 19 COOR> 1 TRP HT1 0.10124 0.57409 -1.38529 TRYP 1 0.00000 X-PLOR> X-PLOR>coor copy end COOR: selected main coordinates copied to comp X-PLOR> X-PLOR>parameter PARRDR> hbonds HBDSET> acceptor=true don=4.7 doff=5.2 dcut=5.7 aon=50.0 aoff=70.0 acut=90.0 HBDSET> end %HBDSET-ERR: inconsistent DCUT, TOLErance, DOFF given. Reset. PARRDR> nbonds NBDSET> atom cdie shift eps=1.0 NBDSET> cutnb=30.0 ctonnb=99.0 ctofnb=99.0 NBDSET> nbxmod=5 vswitch NBDSET> end %NBDSET-ERR: inconsistent CTONNB, CTOFNB given. Reset. %NBDSET-ERR: inconsistent CUTNB, TOLErance, CTOFNB given. Reset. PARRDR>end X-PLOR> X-PLOR> X-PLOR>cons CONS> fix=( name C or name N or name CA ) SELRPN: 3 atoms have been selected out of 19 CONS> interaction=( not (name C or name N or name CA ))=( all ) SELRPN: 16 atoms have been selected out of 19 SELRPN: 19 atoms have been selected out of 19 CONS>end X-PLOR> X-PLOR> X-PLOR>set seed=311. end X-PLOR>dynamics langevin DYNAmics> save=res1.dat isvfrq=20 trajectory=tra1.dat nsavc=2 DYNAmics> nstep=24 timestep=0.001 { [ps] } DYNAmics> iasvel=maxwell firstt=1250.0 nprint=10 DYNAmics> iprfrq=10 ihtfrq=0 ieqfrq=0 DYNAmics> ? DCNTRL: Langevin-Verlet-integrator NSTEp= 24 TIMEstep= 0.0010000 ps DCNTRL-statistics: IPRFrq= 10 DCNTRL-save-options: NSAVC= 2 NSAVV= 0 ISVFrq= 20 NPRInt= 10 DCNTRL-V-assignment: FIRStt= 1250.000 IASVel=MAXW DCNTRL-V-scaling: ISCFrq= 0 HEAT= 1.0000 ISCVel= 0 DCNTRL-CM-options: NTRFrq= 9999999 DCNTRL-heating: IHTFrq= 0 FINAlt= 298.00 IASOrs= 0 TEMInc= 5.00 DCNTRL-equilibration: IEQFrq= 0 ICHEcw= 0 TWINdh= 5.000 TWINdl= -5.000 DCNTRL-langevin: ILBFrq= 0 TBATh= 298.000 RBUF= 0.000 ORIGin=( 0.000000 0.000000 0.000000 ) Verlet algorithm is used. DYNAmics>end ASSFIL: file /home/schwitrs/xplor/test/tra1.dat opened. DYNAMC: number of degrees of freedom= 48 ASSVEL: velocities assigned at 1250.0000 K, SEED= 311.000000 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 3.66855 0.78910 -1.36292 velocity [A/ps] : 0.02560 0.62659 9.37282 ang. mom. [amu A/ps] : -1688.70204 -1976.54530 -1242.19753 kin. ener. [Kcal/mol] : 17.42004 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 3.66855 0.78910 -1.36292 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 MAKINB: mode 5 found 80 exclusions, 20 interactions(1-4) and 60 GB exclusions HBONDS: allocating space for 8 h-bond interactions. HBONDS: 2 distance exclusions and 5 angle exclusions HBONDS: 0 fixed h-bonds, currently 1 h-bonds present --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=-7.139 E(kin)=55.785 temperature=1169.675 | | Etotal =-62.924 grad(E)=12.143 E(BOND)=1.171 E(ANGL)=4.663 | | E(DIHE)=3.599 E(IMPR)=6.918 E(VDW )=-2.173 E(ELEC)=-77.101 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- WRITEC: CORD sets starting from step 2 are written every 2 steps WRITEC: where 16 atoms are "free" HBONDS: allocating space for 4 h-bond interactions. HBONDS: 2 distance exclusions and 5 angle exclusions HBONDS: 0 fixed h-bonds, currently 1 h-bonds present --------------- step= 10 at 0.01000 ps -------------------------------- | E(kin)+E(total)=-6.996 E(kin)=35.736 temperature=749.304 | | Etotal =-42.732 grad(E)=27.197 E(BOND)=8.290 E(ANGL)=18.773 | | E(DIHE)=3.479 E(IMPR)=6.772 E(VDW )=-0.519 E(ELEC)=-79.526 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- averages for last 10 steps ----------------------------- | E(kin)+E(total)=-6.826 E(kin)=37.165 temperature=779.257 | | Etotal =-43.991 grad(E)=33.593 E(BOND)=9.382 E(ANGL)=14.111 | | E(DIHE)=3.517 E(IMPR)=8.928 E(VDW )=-1.150 E(ELEC)=-78.779 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 10 steps ----------------------- | E(kin)+E(total)=0.125 E(kin)=7.650 temperature=160.401 | | Etotal =7.744 grad(E)=6.966 E(BOND)=2.594 E(ANGL)=5.003 | | E(DIHE)=0.046 E(IMPR)=1.611 E(VDW )=0.579 E(ELEC)=0.561 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- HBONDS: allocating space for 4 h-bond interactions. HBONDS: 2 distance exclusions and 5 angle exclusions HBONDS: 0 fixed h-bonds, currently 1 h-bonds present --------------- step= 20 at 0.02000 ps -------------------------------- | E(kin)+E(total)=-6.883 E(kin)=31.570 temperature=661.951 | | Etotal =-38.454 grad(E)=28.883 E(BOND)=6.878 E(ANGL)=12.819 | | E(DIHE)=3.520 E(IMPR)=17.676 E(VDW )=-0.922 E(ELEC)=-78.424 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- averages for last 10 steps ----------------------------- | E(kin)+E(total)=-6.825 E(kin)=28.681 temperature=601.368 | | Etotal =-35.506 grad(E)=31.859 E(BOND)=9.035 E(ANGL)=15.868 | | E(DIHE)=3.562 E(IMPR)=15.854 E(VDW )=-0.853 E(ELEC)=-78.972 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 10 steps ----------------------- | E(kin)+E(total)=0.100 E(kin)=3.998 temperature=83.825 | | Etotal =4.080 grad(E)=2.986 E(BOND)=0.993 E(ANGL)=1.552 | | E(DIHE)=0.037 E(IMPR)=4.713 E(VDW )=0.103 E(ELEC)=0.621 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- averages for last 20 steps ----------------------------- | E(kin)+E(total)=-6.826 E(kin)=32.923 temperature=690.313 | | Etotal =-39.749 grad(E)=32.726 E(BOND)=9.208 E(ANGL)=14.990 | | E(DIHE)=3.539 E(IMPR)=12.391 E(VDW )=-1.001 E(ELEC)=-78.875 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 20 steps ----------------------- | E(kin)+E(total)=0.113 E(kin)=7.433 temperature=155.848 | | Etotal =7.504 grad(E)=5.429 E(BOND)=1.972 E(ANGL)=3.807 | | E(DIHE)=0.047 E(IMPR)=4.939 E(VDW )=0.442 E(ELEC)=0.600 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- ASSFIL: file /home/schwitrs/xplor/test/res1.dat opened. WRIDYN: RESTart file was written at step 20 DCNTRL: restart file written at step= 20 HBONDS: allocating space for 4 h-bond interactions. HBONDS: 2 distance exclusions and 4 angle exclusions HBONDS: 0 fixed h-bonds, currently 2 h-bonds present CENMAS: Information about center of free masses position [A] : 3.67174 0.79575 -1.34715 velocity [A/ps] : 0.32559 0.70479 0.74824 ang. mom. [amu A/ps] : -274.16527 647.65323 -546.32265 kin. ener. [Kcal/mol] : 0.22951 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> X-PLOR>{* first generate a standard trajectory for the following tests *} X-PLOR>{* ============================================================ *} X-PLOR>dynamics langevin DYNAmics> restart=res1.dat ASSFIL: file /home/schwitrs/xplor/test/res1.dat opened. REMARKS FILENAME="/home/schwitrs/xplor/test/res1.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READYN: dynamics restart file was read. Current step= 20 DYNAmics> save=res2.dat isvfrq=20 trajectory=tra2.dat nsavc=2 DYNAmics> nstep=26 timestep=0.001 { [ps] } DYNAmics> nprint=10 DYNAmics> iprfrq=10 ihtfrq=0 ieqfrq=0 DYNAmics> ? DCNTRL: Langevin-Verlet-integrator NSTEp= 26 TIMEstep= 0.0010000 ps DCNTRL-statistics: IPRFrq= 10 DCNTRL-save-options: NSAVC= 2 NSAVV= 0 ISVFrq= 20 NPRInt= 10 DCNTRL-V-assignment: FIRStt= 0.000 IASVel= DCNTRL-V-scaling: ISCFrq= 0 HEAT= 1.0000 ISCVel= 0 DCNTRL-CM-options: NTRFrq= 9999999 DCNTRL-heating: IHTFrq= 0 FINAlt= 298.00 IASOrs= 0 TEMInc= 5.00 DCNTRL-equilibration: IEQFrq= 0 ICHEcw= 0 TWINdh= 5.000 TWINdl= -5.000 DCNTRL-langevin: ILBFrq= 0 TBATh= 298.000 RBUF= 0.000 ORIGin=( 0.000000 0.000000 0.000000 ) Verlet algorithm is used. DYNAmics>end ASSFIL: file /home/schwitrs/xplor/test/tra2.dat opened. DYNAMC: number of degrees of freedom= 48 ------------------------------------------------------------------------------- DYNLNG: energies from restart file: | Etotal =-38.454 grad(E)=28.883 E(BOND)=6.878 E(ANGL)=12.819 | | E(DIHE)=3.520 E(IMPR)=17.676 E(VDW )=-0.922 E(ELEC)=-78.424 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- DYNLNG: no initialization; re-evaluated energies: | Etotal =-38.454 grad(E)=28.883 E(BOND)=6.878 E(ANGL)=12.819 | | E(DIHE)=3.520 E(IMPR)=17.676 E(VDW )=-0.922 E(ELEC)=-78.424 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- WRITEC: CORD sets starting from step 22 are written every 2 steps WRITEC: where 16 atoms are "free" HBONDS: allocating space for 5 h-bond interactions. HBONDS: 2 distance exclusions and 4 angle exclusions HBONDS: 0 fixed h-bonds, currently 2 h-bonds present --------------- step= 30 at 0.03000 ps -------------------------------- | E(kin)+E(total)=-6.753 E(kin)=32.555 temperature=682.610 | | Etotal =-39.308 grad(E)=35.982 E(BOND)=11.541 E(ANGL)=16.319 | | E(DIHE)=2.860 E(IMPR)=10.468 E(VDW )=-0.256 E(ELEC)=-80.240 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- averages for last 10 steps ----------------------------- | E(kin)+E(total)=-6.854 E(kin)=35.665 temperature=747.805 | | Etotal =-42.519 grad(E)=31.085 E(BOND)=10.605 E(ANGL)=12.269 | | E(DIHE)=3.117 E(IMPR)=11.933 E(VDW )=-0.536 E(ELEC)=-79.907 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 10 steps ----------------------- | E(kin)+E(total)=0.104 E(kin)=2.774 temperature=58.169 | | Etotal =2.860 grad(E)=4.444 E(BOND)=2.115 E(ANGL)=2.220 | | E(DIHE)=0.203 E(IMPR)=1.386 E(VDW )=0.223 E(ELEC)=0.485 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- averages for last 30 steps ----------------------------- | E(kin)+E(total)=-6.835 E(kin)=33.837 temperature=709.477 | | Etotal =-40.672 grad(E)=32.179 E(BOND)=9.674 E(ANGL)=14.083 | | E(DIHE)=3.399 E(IMPR)=12.238 E(VDW )=-0.846 E(ELEC)=-79.219 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 30 steps ----------------------- | E(kin)+E(total)=0.111 E(kin)=6.408 temperature=134.369 | | Etotal =6.478 grad(E)=5.180 E(BOND)=2.125 E(ANGL)=3.598 | | E(DIHE)=0.234 E(IMPR)=4.117 E(VDW )=0.441 E(ELEC)=0.745 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- HBONDS: allocating space for 5 h-bond interactions. HBONDS: 2 distance exclusions and 4 angle exclusions HBONDS: 0 fixed h-bonds, currently 2 h-bonds present --------------- step= 40 at 0.04000 ps -------------------------------- | E(kin)+E(total)=-6.730 E(kin)=31.433 temperature=659.072 | | Etotal =-38.162 grad(E)=37.083 E(BOND)=8.991 E(ANGL)=13.346 | | E(DIHE)=2.348 E(IMPR)=15.257 E(VDW )=-1.506 E(ELEC)=-76.598 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- averages for last 10 steps ----------------------------- | E(kin)+E(total)=-6.867 E(kin)=39.182 temperature=821.554 | | Etotal =-46.049 grad(E)=30.663 E(BOND)=6.265 E(ANGL)=15.502 | | E(DIHE)=2.681 E(IMPR)=9.137 E(VDW )=-0.819 E(ELEC)=-78.815 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 10 steps ----------------------- | E(kin)+E(total)=0.089 E(kin)=4.391 temperature=92.062 | | Etotal =4.472 grad(E)=3.924 E(BOND)=2.743 E(ANGL)=1.243 | | E(DIHE)=0.164 E(IMPR)=3.329 E(VDW )=0.429 E(ELEC)=1.343 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- averages for last 40 steps ----------------------------- | E(kin)+E(total)=-6.843 E(kin)=35.173 temperature=737.496 | | Etotal =-42.016 grad(E)=31.800 E(BOND)=8.822 E(ANGL)=14.438 | | E(DIHE)=3.219 E(IMPR)=11.463 E(VDW )=-0.839 E(ELEC)=-79.118 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 40 steps ----------------------- | E(kin)+E(total)=0.107 E(kin)=6.401 temperature=134.221 | | Etotal =6.473 grad(E)=4.940 E(BOND)=2.729 E(ANGL)=3.237 | | E(DIHE)=0.380 E(IMPR)=4.158 E(VDW )=0.438 E(ELEC)=0.947 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- ASSFIL: file /home/schwitrs/xplor/test/res2.dat opened. WRIDYN: RESTart file was written at step 40 DCNTRL: restart file written at step= 40 HBONDS: allocating space for 5 h-bond interactions. HBONDS: 2 distance exclusions and 5 angle exclusions HBONDS: 0 fixed h-bonds, currently 1 h-bonds present CENMAS: Information about center of free masses position [A] : 3.68640 0.81111 -1.35142 velocity [A/ps] : 0.38139 1.61610 0.15882 ang. mom. [amu A/ps] : -300.27282 249.38714 -567.15403 kin. ener. [Kcal/mol] : 0.54928 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR>open res1.dat access=append end close res1.dat disp=delete end ASSFIL: file /home/schwitrs/xplor/test/res1.dat opened. X-PLOR> X-PLOR> X-PLOR> X-PLOR> X-PLOR>dynamics langevin DYNAmics> restart=res2.dat ASSFIL: file /home/schwitrs/xplor/test/res2.dat opened. REMARKS FILENAME="/home/schwitrs/xplor/test/res2.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READYN: dynamics restart file was read. Current step= 40 DYNAmics> save=res3.dat isvfrq=20 trajectory=tra3.dat nsavc=2 DYNAmics> nstep=28 timestep=0.001 { [ps] } DYNAmics> nprint=10 DYNAmics> iprfrq=10 ihtfrq=0 ieqfrq=0 DYNAmics> ? DCNTRL: Langevin-Verlet-integrator NSTEp= 28 TIMEstep= 0.0010000 ps DCNTRL-statistics: IPRFrq= 10 DCNTRL-save-options: NSAVC= 2 NSAVV= 0 ISVFrq= 20 NPRInt= 10 DCNTRL-V-assignment: FIRStt= 0.000 IASVel= DCNTRL-V-scaling: ISCFrq= 0 HEAT= 1.0000 ISCVel= 0 DCNTRL-CM-options: NTRFrq= 9999999 DCNTRL-heating: IHTFrq= 0 FINAlt= 298.00 IASOrs= 0 TEMInc= 5.00 DCNTRL-equilibration: IEQFrq= 0 ICHEcw= 0 TWINdh= 5.000 TWINdl= -5.000 DCNTRL-langevin: ILBFrq= 0 TBATh= 298.000 RBUF= 0.000 ORIGin=( 0.000000 0.000000 0.000000 ) Verlet algorithm is used. DYNAmics>end ASSFIL: file /home/schwitrs/xplor/test/tra3.dat opened. DYNAMC: number of degrees of freedom= 48 ------------------------------------------------------------------------------- DYNLNG: energies from restart file: | Etotal =-38.162 grad(E)=37.083 E(BOND)=8.991 E(ANGL)=13.346 | | E(DIHE)=2.348 E(IMPR)=15.257 E(VDW )=-1.506 E(ELEC)=-76.598 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- DYNLNG: no initialization; re-evaluated energies: | Etotal =-38.162 grad(E)=37.083 E(BOND)=8.991 E(ANGL)=13.346 | | E(DIHE)=2.348 E(IMPR)=15.257 E(VDW )=-1.506 E(ELEC)=-76.598 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- WRITEC: CORD sets starting from step 42 are written every 2 steps WRITEC: where 16 atoms are "free" --------------- step= 50 at 0.05000 ps -------------------------------- | E(kin)+E(total)=-6.706 E(kin)=27.461 temperature=575.783 | | Etotal =-34.166 grad(E)=39.496 E(BOND)=6.351 E(ANGL)=23.715 | | E(DIHE)=1.261 E(IMPR)=13.945 E(VDW )=-1.939 E(ELEC)=-77.501 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- averages for last 10 steps ----------------------------- | E(kin)+E(total)=-6.815 E(kin)=29.776 temperature=624.324 | | Etotal =-36.590 grad(E)=34.080 E(BOND)=9.313 E(ANGL)=17.437 | | E(DIHE)=1.716 E(IMPR)=13.396 E(VDW )=-1.773 E(ELEC)=-76.679 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 10 steps ----------------------- | E(kin)+E(total)=0.065 E(kin)=1.434 temperature=30.058 | | Etotal =1.491 grad(E)=3.581 E(BOND)=1.956 E(ANGL)=4.035 | | E(DIHE)=0.315 E(IMPR)=1.216 E(VDW )=0.090 E(ELEC)=0.406 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- averages for last 50 steps ----------------------------- | E(kin)+E(total)=-6.837 E(kin)=34.094 temperature=714.862 | | Etotal =-40.931 grad(E)=32.256 E(BOND)=8.920 E(ANGL)=15.037 | | E(DIHE)=2.919 E(IMPR)=11.850 E(VDW )=-1.026 E(ELEC)=-78.630 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 50 steps ----------------------- | E(kin)+E(total)=0.100 E(kin)=6.153 temperature=129.005 | | Etotal =6.219 grad(E)=4.787 E(BOND)=2.600 E(ANGL)=3.616 | | E(DIHE)=0.705 E(IMPR)=3.837 E(VDW )=0.543 E(ELEC)=1.305 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- HBONDS: allocating space for 4 h-bond interactions. HBONDS: 2 distance exclusions and 5 angle exclusions HBONDS: 0 fixed h-bonds, currently 1 h-bonds present --------------- step= 60 at 0.06000 ps -------------------------------- | E(kin)+E(total)=-6.779 E(kin)=39.687 temperature=832.141 | | Etotal =-46.466 grad(E)=35.531 E(BOND)=9.470 E(ANGL)=10.679 | | E(DIHE)=0.773 E(IMPR)=10.858 E(VDW )=-2.159 E(ELEC)=-76.087 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- averages for last 10 steps ----------------------------- | E(kin)+E(total)=-6.870 E(kin)=40.941 temperature=858.429 | | Etotal =-47.811 grad(E)=31.012 E(BOND)=5.423 E(ANGL)=16.196 | | E(DIHE)=0.938 E(IMPR)=9.175 E(VDW )=-2.138 E(ELEC)=-77.405 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 10 steps ----------------------- | E(kin)+E(total)=0.071 E(kin)=5.748 temperature=120.521 | | Etotal =5.809 grad(E)=4.787 E(BOND)=1.945 E(ANGL)=4.654 | | E(DIHE)=0.133 E(IMPR)=2.459 E(VDW )=0.069 E(ELEC)=0.666 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- averages for last 60 steps ----------------------------- | E(kin)+E(total)=-6.843 E(kin)=35.235 temperature=738.789 | | Etotal =-42.078 grad(E)=32.049 E(BOND)=8.337 E(ANGL)=15.231 | | E(DIHE)=2.588 E(IMPR)=11.404 E(VDW )=-1.211 E(ELEC)=-78.426 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 60 steps ----------------------- | E(kin)+E(total)=0.097 E(kin)=6.600 temperature=138.391 | | Etotal =6.665 grad(E)=4.810 E(BOND)=2.822 E(ANGL)=3.833 | | E(DIHE)=0.981 E(IMPR)=3.778 E(VDW )=0.647 E(ELEC)=1.304 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- ASSFIL: file /home/schwitrs/xplor/test/res3.dat opened. WRIDYN: RESTart file was written at step 60 DCNTRL: restart file written at step= 60 CENMAS: Information about center of free masses position [A] : 3.70521 0.82881 -1.34631 velocity [A/ps] : 0.95901 -0.42569 -0.59893 ang. mom. [amu A/ps] : -17.57381 190.35587 599.11235 kin. ener. [Kcal/mol] : 0.28815 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR>open res2.dat access=append end close res2.dat disp=delete end ASSFIL: file /home/schwitrs/xplor/test/res2.dat opened. X-PLOR>open res3.dat access=append end close res3.dat disp=delete end ASSFIL: file /home/schwitrs/xplor/test/res3.dat opened. X-PLOR> X-PLOR> X-PLOR> X-PLOR>{* test average and rms fluctuation calculation *} X-PLOR>{* ============================================ *} X-PLOR>dynamics analysis average AVECOR> input=tra1.dat ASSFIL: file /home/schwitrs/xplor/test/tra1.dat opened. AVECOR> input=tra2.dat ASSFIL: file /home/schwitrs/xplor/test/tra2.dat opened. AVECOR> input=tra3.dat ASSFIL: file /home/schwitrs/xplor/test/tra3.dat opened. AVECOR> begin=4 skip=4 stop=60 AVECOR>end REMARKS FILENAME="/home/schwitrs/xplor/test/tra1.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 2 READC: 16 atoms were "free" READC: NUNIt= 3 READC: BEGIn= 4 SKIP= 4 STOP= 60 READC: TIMEstep= 0.00100000 ps header= CORD READC: EOF on file= 1 while trying to read step= 26 REMARKS FILENAME="/home/schwitrs/xplor/test/tra2.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 2 ISTART= 22 READC: 16 atoms were "free" READC: mismatch correction; file-number= 2 READC: EOF on file= 2 while trying to read step= 48 REMARKS FILENAME="/home/schwitrs/xplor/test/tra3.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 3 ISTART= 42 READC: 16 atoms were "free" READC: mismatch correction; file-number= 3 READC: complete. 15 coordinate sets were passed to calling routine AVECOR: average set and RMS have been copied to main set. X-PLOR>rewind tra1.dat end MISCOM: rewinding file /home/schwitrs/xplor/test/tra1.dat X-PLOR>rewind tra2.dat end MISCOM: rewinding file /home/schwitrs/xplor/test/tra2.dat X-PLOR>rewind tra3.dat end MISCOM: rewinding file /home/schwitrs/xplor/test/tra3.dat X-PLOR> X-PLOR>{* test rms covariance calculation *} X-PLOR>{* =============================== *} X-PLOR>dynamics analysis covariance COVAR> input=tra1.dat COVAR> input=tra2.dat COVAR> input=tra3.dat COVAR> begin=4 skip=4 stop=60 COVAR> set1=( name CB or name CG ) SELRPN: 2 atoms have been selected out of 19 COVAR> set2=( not ( name C or name N or name CA ) ) SELRPN: 16 atoms have been selected out of 19 COVAR>end REMARKS FILENAME="/home/schwitrs/xplor/test/tra1.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 2 READC: 16 atoms were "free" READC: NUNIt= 3 READC: BEGIn= 4 SKIP= 4 STOP= 60 READC: TIMEstep= 0.00100000 ps header= CORD READC: EOF on file= 1 while trying to read step= 26 REMARKS FILENAME="/home/schwitrs/xplor/test/tra2.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 2 ISTART= 22 READC: 16 atoms were "free" READC: mismatch correction; file-number= 2 READC: EOF on file= 2 while trying to read step= 48 REMARKS FILENAME="/home/schwitrs/xplor/test/tra3.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 3 ISTART= 42 READC: 16 atoms were "free" READC: mismatch correction; file-number= 3 READC: complete. 15 coordinate sets were passed to calling routine REMARKS FILENAME="stdout" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs COVARIANCE MATRIX NSET1= 2 1=(TRYP 1 TRP CB ) 2=(TRYP 1 TRP CG ) NSET2= 16 1=(TRYP 1 TRP HT1 ) 2=(TRYP 1 TRP HT2 ) 3=(TRYP 1 TRP HT3 ) 4=(TRYP 1 TRP CB ) 5=(TRYP 1 TRP CG ) 6=(TRYP 1 TRP CD2 ) 7=(TRYP 1 TRP CE2 ) 8=(TRYP 1 TRP CE3 ) 9=(TRYP 1 TRP CD1 ) 10=(TRYP 1 TRP NE1 ) 11=(TRYP 1 TRP HE1 ) 12=(TRYP 1 TRP CZ2 ) 13=(TRYP 1 TRP CZ3 ) 14=(TRYP 1 TRP CH2 ) 15=(TRYP 1 TRP OT1 ) 16=(TRYP 1 TRP OT2 ) 0.21293635 -0.28998957 -0.94771857E-01 1.0000000 0.25858592 0.45449497E-02 -0.59150028 0.31760532 -0.23335827 -0.74512215E-01 0.34455334 -0.43743137 -0.10856014 0.82234920E-01 0.17177168 -0.30274888 0.96184099E-01 -0.12921482 0.19788346 0.25858592 1.0000000 0.29943104 -0.16436586 -0.13559505 0.56519247 -0.21327765 0.41850238E-01 -0.19253510 -0.67268340 -0.83212020E-01 -0.14199701 0.58681657E-01 X-PLOR> X-PLOR>write coor end REMARK FILENAME="stdout" REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARK AND CG 50 STEPS REMARK EPS=R POTENTIAL REMARK DATE:11-Jun-07 15:21:40 created by user: schwitrs ATOM 1 HT1 TRP 1 0.071 0.354 -1.144 1.00 0.32 TRYP ATOM 2 HT2 TRP 1 1.364 0.754 -1.911 1.00 0.37 TRYP ATOM 3 N TRP 1 1.067 0.302 -1.101 1.00 0.00 TRYP ATOM 4 HT3 TRP 1 1.407 -0.611 -1.036 1.00 0.35 TRYP ATOM 5 CA TRP 1 1.472 1.192 0.027 1.00 0.00 TRYP ATOM 6 CB TRP 1 2.709 1.980 -0.311 1.00 0.07 TRYP ATOM 7 CG TRP 1 3.910 1.087 -0.611 1.00 0.10 TRYP ATOM 8 CD2 TRP 1 4.255 0.608 -1.843 1.00 0.07 TRYP ATOM 9 CE2 TRP 1 5.432 -0.060 -1.585 1.00 0.06 TRYP ATOM 10 CE3 TRP 1 3.752 0.726 -3.122 1.00 0.08 TRYP ATOM 11 CD1 TRP 1 4.818 0.738 0.355 1.00 0.11 TRYP ATOM 12 NE1 TRP 1 5.741 0.060 -0.278 1.00 0.08 TRYP ATOM 13 HE1 TRP 1 6.433 -0.239 0.079 1.00 0.55 TRYP ATOM 14 CZ2 TRP 1 6.127 -0.636 -2.620 1.00 0.10 TRYP ATOM 15 CZ3 TRP 1 4.453 0.172 -4.170 1.00 0.08 TRYP ATOM 16 CH2 TRP 1 5.619 -0.514 -3.899 1.00 0.09 TRYP ATOM 17 C TRP 1 0.280 2.113 0.309 1.00 0.00 TRYP ATOM 18 OT1 TRP 1 -0.455 2.377 -0.641 1.00 0.07 TRYP ATOM 19 OT2 TRP 1 0.098 2.493 1.438 1.00 0.21 TRYP END X-PLOR> X-PLOR>{* test trajectory merging *} X-PLOR>{* ======================= *} X-PLOR>dynamics merge MERGE> input=tra1.dat MERGE> input=tra2.dat MERGE> input=tra3.dat MERGE> begin=2 skip=2 stop=60 MERGE> output=trat.dat MERGE>end ASSFIL: file /home/schwitrs/xplor/test/trat.dat opened. REMARKS FILENAME="/home/schwitrs/xplor/test/tra1.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 2 READC: 16 atoms were "free" READC: NUNIt= 3 READC: BEGIn= 2 SKIP= 2 STOP= 60 READC: TIMEstep= 0.00100000 ps header= CORD WRITEC: CORD sets starting from step 2 are written every 2 steps WRITEC: where 16 atoms are "free" READC: EOF on file= 1 while trying to read step= 26 REMARKS FILENAME="/home/schwitrs/xplor/test/tra2.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 2 ISTART= 22 READC: 16 atoms were "free" READC: mismatch correction; file-number= 2 READC: EOF on file= 2 while trying to read step= 48 REMARKS FILENAME="/home/schwitrs/xplor/test/tra3.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 3 ISTART= 42 READC: 16 atoms were "free" READC: mismatch correction; file-number= 3 READC: complete. 30 coordinate sets were passed to calling routine X-PLOR>rewind tra1.dat end MISCOM: rewinding file /home/schwitrs/xplor/test/tra1.dat X-PLOR>rewind tra2.dat end MISCOM: rewinding file /home/schwitrs/xplor/test/tra2.dat X-PLOR>rewind tra3.dat end MISCOM: rewinding file /home/schwitrs/xplor/test/tra3.dat X-PLOR> X-PLOR> X-PLOR>{* test merging and re-orienting *} X-PLOR>{* ============================= *} X-PLOR>dynamics merge MERGE> input=tra1.dat MERGE> input=tra2.dat MERGE> input=tra3.dat MERGE> begin=2 skip=2 stop=60 MERGE> output=trar.dat MERGE> orient ORIENT> massweighted=true ORIENT> selection=( not ( name C or name CA or name N ) ) SELRPN: 16 atoms have been selected out of 19 ORIENT> end MERGE>end ASSFIL: file /home/schwitrs/xplor/test/trar.dat opened. MERGE: output-trajectory oriented with respect to main coordinate set MERGE: MASSweighting=T NO-ROtation=F wmainWEIGhting=F REMARKS FILENAME="/home/schwitrs/xplor/test/tra1.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 2 READC: 16 atoms were "free" READC: NUNIt= 3 READC: BEGIn= 2 SKIP= 2 STOP= 60 READC: TIMEstep= 0.00100000 ps header= CORD WRITEC: CORD sets starting from step 2 are written every 2 steps WRITEC: where 16 atoms are "free" READC: EOF on file= 1 while trying to read step= 26 REMARKS FILENAME="/home/schwitrs/xplor/test/tra2.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 2 ISTART= 22 READC: 16 atoms were "free" READC: mismatch correction; file-number= 2 READC: EOF on file= 2 while trying to read step= 48 REMARKS FILENAME="/home/schwitrs/xplor/test/tra3.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 3 ISTART= 42 READC: 16 atoms were "free" READC: mismatch correction; file-number= 3 READC: complete. 30 coordinate sets were passed to calling routine X-PLOR>close tra1.dat end X-PLOR>close tra2.dat end X-PLOR>close tra3.dat end X-PLOR>open tra1.dat access=append end close tra1.dat disp=delete end ASSFIL: file /home/schwitrs/xplor/test/tra1.dat opened. X-PLOR>open tra2.dat access=append end close tra2.dat disp=delete end ASSFIL: file /home/schwitrs/xplor/test/tra2.dat opened. X-PLOR>open tra3.dat access=append end close tra3.dat disp=delete end ASSFIL: file /home/schwitrs/xplor/test/tra3.dat opened. X-PLOR> X-PLOR>dynamics analysis average AVECOR> input=trat.dat ASSFIL: file /home/schwitrs/xplor/test/trat.dat opened. AVECOR> begin=4 skip=4 stop=60 AVECOR>end REMARKS FILENAME="/home/schwitrs/xplor/test/trat.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 2 READC: 16 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 4 SKIP= 4 STOP= 60 READC: TIMEstep= 0.00100000 ps header= CORD READC: complete. 15 coordinate sets were passed to calling routine AVECOR: average set and RMS have been copied to main set. X-PLOR>rewind trat.dat end MISCOM: rewinding file /home/schwitrs/xplor/test/trat.dat X-PLOR>write coor end REMARK FILENAME="stdout" REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARK AND CG 50 STEPS REMARK EPS=R POTENTIAL REMARK DATE:11-Jun-07 15:21:40 created by user: schwitrs ATOM 1 HT1 TRP 1 0.071 0.354 -1.144 1.00 0.32 TRYP ATOM 2 HT2 TRP 1 1.364 0.754 -1.911 1.00 0.37 TRYP ATOM 3 N TRP 1 1.067 0.302 -1.101 1.00 0.00 TRYP ATOM 4 HT3 TRP 1 1.407 -0.611 -1.036 1.00 0.35 TRYP ATOM 5 CA TRP 1 1.472 1.192 0.027 1.00 0.00 TRYP ATOM 6 CB TRP 1 2.709 1.980 -0.311 1.00 0.07 TRYP ATOM 7 CG TRP 1 3.910 1.087 -0.611 1.00 0.10 TRYP ATOM 8 CD2 TRP 1 4.255 0.608 -1.843 1.00 0.07 TRYP ATOM 9 CE2 TRP 1 5.432 -0.060 -1.585 1.00 0.06 TRYP ATOM 10 CE3 TRP 1 3.752 0.726 -3.122 1.00 0.08 TRYP ATOM 11 CD1 TRP 1 4.818 0.738 0.355 1.00 0.11 TRYP ATOM 12 NE1 TRP 1 5.741 0.060 -0.278 1.00 0.08 TRYP ATOM 13 HE1 TRP 1 6.433 -0.239 0.079 1.00 0.55 TRYP ATOM 14 CZ2 TRP 1 6.127 -0.636 -2.620 1.00 0.10 TRYP ATOM 15 CZ3 TRP 1 4.453 0.172 -4.170 1.00 0.08 TRYP ATOM 16 CH2 TRP 1 5.619 -0.514 -3.899 1.00 0.09 TRYP ATOM 17 C TRP 1 0.280 2.113 0.309 1.00 0.00 TRYP ATOM 18 OT1 TRP 1 -0.455 2.377 -0.641 1.00 0.07 TRYP ATOM 19 OT2 TRP 1 0.098 2.493 1.438 1.00 0.21 TRYP END X-PLOR>coor rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.238169, square sum= 1.0778, denominator= 19.0000 X-PLOR> X-PLOR> X-PLOR>dynamics analysis average AVECOR> input=trat.dat AVECOR> begin=10 stop=10 AVECOR>end REMARKS FILENAME="/home/schwitrs/xplor/test/trat.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 2 READC: 16 atoms were "free" READC: SKIP not compatible. Modified READC: NUNIt= 1 READC: BEGIn= 10 SKIP= 2 STOP= 10 READC: TIMEstep= 0.00100000 ps header= CORD READC: complete. 1 coordinate sets were passed to calling routine AVECOR: average set and RMS have been copied to main set. X-PLOR> X-PLOR>coor fit COOR-FIT > mass=true selection=( not ( name C or name CA or name N ) ) SELRPN: 16 atoms have been selected out of 19 COOR: using atom subset. COOR-FIT >end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.0039 -0.0048 -0.0101) Rotation matrix = 0.999998 -0.000639 -0.001811 0.000637 0.999999 -0.001192 0.001812 0.001190 0.999998 Corresp. Eulerian angles (theta1,theta2,theta3) 123.3093 0.1242 236.6542 Corresp. spherical polar angles (psi,phi,kappa) 36.7177 151.8387 0.1295 Corresp. rotation angle 0.1295 about axis -0.5271 0.8016 -0.2822 Corresp. quaternions 1.0000 -0.0006 0.0009 -0.0003 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.1163 X-PLOR> X-PLOR>dynamics analysis average AVECOR> input=trar.dat ASSFIL: file /home/schwitrs/xplor/test/trar.dat opened. AVECOR> begin=10 stop=10 AVECOR>end REMARKS FILENAME="/home/schwitrs/xplor/test/trar.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 2 READC: 16 atoms were "free" READC: SKIP not compatible. Modified READC: NUNIt= 1 READC: BEGIn= 10 SKIP= 2 STOP= 10 READC: TIMEstep= 0.00100000 ps header= CORD READC: complete. 1 coordinate sets were passed to calling routine AVECOR: average set and RMS have been copied to main set. X-PLOR> X-PLOR>close trar.dat end X-PLOR>open trar.dat access=append end close trar.dat disp=delete end ASSFIL: file /home/schwitrs/xplor/test/trar.dat opened. X-PLOR> X-PLOR>coor fit COOR-FIT > mass=true selection=( not ( name C or name CA or name N ) ) SELRPN: 16 atoms have been selected out of 19 COOR: using atom subset. COOR-FIT >end Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( -0.0226 -0.0460 -0.0638) Rotation matrix = 0.999924 -0.004375 -0.011550 0.004239 0.999921 -0.011816 0.011600 0.011766 0.999863 Corresp. Eulerian angles (theta1,theta2,theta3) 135.4070 0.9468 224.3462 Corresp. spherical polar angles (psi,phi,kappa) 47.3216 159.9353 0.9784 Corresp. rotation angle 0.9784 about axis -0.6905 0.6779 -0.2522 Corresp. quaternions 1.0000 -0.0059 0.0058 -0.0022 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.1163 X-PLOR> X-PLOR>{ now test the protable dynamics trajectory file } X-PLOR>{ ============================================== } X-PLOR>coor init end COOR: selected main coordinates initialized X-PLOR> X-PLOR>rewind trat.dat end MISCOM: rewinding file /home/schwitrs/xplor/test/trat.dat X-PLOR>dynamics merge MERGE> ascii=false input=trat.dat begin=2 skip=2 stop=60 MERGE> oascii=true scale=100000 offset=800 format=10Z7 MERGE> output=traf.dat MERGE>end ASSFIL: file /home/schwitrs/xplor/test/traf.dat opened. REMARKS FILENAME="/home/schwitrs/xplor/test/trat.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 2 READC: 16 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 2 SKIP= 2 STOP= 60 READC: TIMEstep= 0.00100000 ps header= CORD WRITEC: CORD sets starting from step 2 are written every 2 steps WRITEC: where 16 atoms are "free" READC: complete. 30 coordinate sets were passed to calling routine X-PLOR>close trat.dat end X-PLOR>open trat.dat access=append end close trat.dat disp=delete end ASSFIL: file /home/schwitrs/xplor/test/trat.dat opened. X-PLOR> X-PLOR>coor init end COOR: selected main coordinates initialized X-PLOR> X-PLOR>dynamics merge MERGE> ascii=true input=traf.dat ASSFIL: file /home/schwitrs/xplor/test/traf.dat opened. MERGE> oascii=false output=tran.dat MERGE>end ASSFIL: file /home/schwitrs/xplor/test/tran.dat opened. REMARKS FILENAME="/home/schwitrs/xplor/test/traf.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 2 READC: 16 atoms were "free" READC: BEGIN not compatible. Modified READC: SKIP not compatible. Modified READC: STOP not compatible. Modified READC: NUNIt= 1 READC: BEGIn= 2 SKIP= 2 STOP= 999998 READC: TIMEstep= 0.00100000 ps header= CORD WRITEC: CORD sets starting from step 2 are written every 2 steps WRITEC: where 16 atoms are "free" READC: EOF on file= 1 while trying to read step= 62 %READC-EOF file 1 at step 62 READC: complete. 30 coordinate sets were passed to calling routine X-PLOR> X-PLOR>close traf.dat end X-PLOR>open traf.dat access=append end close traf.dat disp=delete end ASSFIL: file /home/schwitrs/xplor/test/traf.dat opened. X-PLOR> X-PLOR> X-PLOR>dynamics anal average AVECOR> input=tran.dat ASSFIL: file /home/schwitrs/xplor/test/tran.dat opened. AVECOR> begin=4 skip=4 stop=60 AVECOR>end REMARKS FILENAME="/home/schwitrs/xplor/test/tran.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 2 READC: 16 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 4 SKIP= 4 STOP= 60 READC: TIMEstep= 0.00100000 ps header= CORD READC: complete. 15 coordinate sets were passed to calling routine AVECOR: average set and RMS have been copied to main set. X-PLOR> X-PLOR>write coor end REMARK FILENAME="stdout" REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARK AND CG 50 STEPS REMARK EPS=R POTENTIAL REMARK DATE:11-Jun-07 15:21:40 created by user: schwitrs ATOM 1 HT1 TRP 1 0.071 0.354 -1.144 1.00 0.32 TRYP ATOM 2 HT2 TRP 1 1.364 0.754 -1.911 1.00 0.37 TRYP ATOM 3 N TRP 1 1.067 0.302 -1.101 1.00 0.00 TRYP ATOM 4 HT3 TRP 1 1.407 -0.611 -1.036 1.00 0.35 TRYP ATOM 5 CA TRP 1 1.472 1.192 0.027 1.00 0.00 TRYP ATOM 6 CB TRP 1 2.709 1.980 -0.311 1.00 0.07 TRYP ATOM 7 CG TRP 1 3.910 1.087 -0.611 1.00 0.10 TRYP ATOM 8 CD2 TRP 1 4.255 0.608 -1.843 1.00 0.07 TRYP ATOM 9 CE2 TRP 1 5.432 -0.060 -1.585 1.00 0.06 TRYP ATOM 10 CE3 TRP 1 3.752 0.726 -3.122 1.00 0.08 TRYP ATOM 11 CD1 TRP 1 4.818 0.738 0.355 1.00 0.11 TRYP ATOM 12 NE1 TRP 1 5.740 0.060 -0.278 1.00 0.08 TRYP ATOM 13 HE1 TRP 1 6.433 -0.239 0.079 1.00 0.55 TRYP ATOM 14 CZ2 TRP 1 6.127 -0.636 -2.620 1.00 0.10 TRYP ATOM 15 CZ3 TRP 1 4.453 0.172 -4.170 1.00 0.08 TRYP ATOM 16 CH2 TRP 1 5.619 -0.514 -3.899 1.00 0.09 TRYP ATOM 17 C TRP 1 0.280 2.113 0.309 1.00 0.00 TRYP ATOM 18 OT1 TRP 1 -0.455 2.377 -0.641 1.00 0.07 TRYP ATOM 19 OT2 TRP 1 0.098 2.493 1.438 1.00 0.21 TRYP END X-PLOR> X-PLOR>rewind tran.dat end MISCOM: rewinding file /home/schwitrs/xplor/test/tran.dat X-PLOR> X-PLOR>dynamics anal average AVECOR> input=tran.dat AVECOR> begin=4 skip=4 stop=60 reference=comp AVECOR>end AVECOR: RMS computed wrt. comparison set REMARKS FILENAME="/home/schwitrs/xplor/test/tran.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 2 READC: 16 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 4 SKIP= 4 STOP= 60 READC: TIMEstep= 0.00100000 ps header= CORD READC: complete. 15 coordinate sets were passed to calling routine AVECOR: average set and RMS have been copied to main set. X-PLOR> X-PLOR>close tran.dat end X-PLOR>open tran.dat access=append end close tran.dat disp=delete end ASSFIL: file /home/schwitrs/xplor/test/tran.dat opened. X-PLOR> X-PLOR>write coor end REMARK FILENAME="stdout" REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARK AND CG 50 STEPS REMARK EPS=R POTENTIAL REMARK DATE:11-Jun-07 15:21:40 created by user: schwitrs ATOM 1 HT1 TRP 1 0.071 0.354 -1.144 1.00 0.45 TRYP ATOM 2 HT2 TRP 1 1.364 0.754 -1.911 1.00 0.60 TRYP ATOM 3 N TRP 1 1.067 0.302 -1.101 1.00 0.00 TRYP ATOM 4 HT3 TRP 1 1.407 -0.611 -1.036 1.00 0.54 TRYP ATOM 5 CA TRP 1 1.472 1.192 0.027 1.00 0.00 TRYP ATOM 6 CB TRP 1 2.709 1.980 -0.311 1.00 0.09 TRYP ATOM 7 CG TRP 1 3.910 1.087 -0.611 1.00 0.15 TRYP ATOM 8 CD2 TRP 1 4.255 0.608 -1.843 1.00 0.12 TRYP ATOM 9 CE2 TRP 1 5.432 -0.060 -1.585 1.00 0.08 TRYP ATOM 10 CE3 TRP 1 3.752 0.726 -3.122 1.00 0.10 TRYP ATOM 11 CD1 TRP 1 4.818 0.738 0.355 1.00 0.13 TRYP ATOM 12 NE1 TRP 1 5.740 0.060 -0.278 1.00 0.09 TRYP ATOM 13 HE1 TRP 1 6.433 -0.239 0.079 1.00 0.82 TRYP ATOM 14 CZ2 TRP 1 6.127 -0.636 -2.620 1.00 0.12 TRYP ATOM 15 CZ3 TRP 1 4.453 0.172 -4.170 1.00 0.10 TRYP ATOM 16 CH2 TRP 1 5.619 -0.514 -3.899 1.00 0.14 TRYP ATOM 17 C TRP 1 0.280 2.113 0.309 1.00 0.00 TRYP ATOM 18 OT1 TRP 1 -0.455 2.377 -0.641 1.00 0.14 TRYP ATOM 19 OT2 TRP 1 0.098 2.493 1.438 1.00 0.42 TRYP END X-PLOR> X-PLOR>coor swap end COOR: selected coordinates swaped (main<->comp) X-PLOR> X-PLOR>{* now test the selected trajectory generation *} X-PLOR>{* =========================================== *} X-PLOR>{* first generate a standard trajectory for the following tests *} X-PLOR>{* ============================================================ *} X-PLOR> X-PLOR>set seed=311. end X-PLOR>dynamics langevin DYNAmics> isvfrq=0 DYNAmics> trajectory=tracrd.dat nsavc=2 cselection=( name ot1 or name cb ) SELRPN: 2 atoms have been selected out of 19 DYNAmics> velocity=travel.dat nsavv=4 vselection=( name ot1 or name cg ) SELRPN: 2 atoms have been selected out of 19 DYNAmics> iasvel=maxwell firstt=1250.0 nprint=0 DYNAmics> nstep=60 timestep=0.001 { [ps] } DYNAmics> iprfrq=0 ihtfrq=0 ieqfrq=0 DYNAmics> ? DCNTRL: Langevin-Verlet-integrator NSTEp= 60 TIMEstep= 0.0010000 ps DCNTRL-statistics: IPRFrq= 0 DCNTRL-save-options: NSAVC= 2 NSAVV= 4 ISVFrq= 0 NPRInt= 0 DCNTRL-V-assignment: FIRStt= 1250.000 IASVel=MAXW DCNTRL-V-scaling: ISCFrq= 0 HEAT= 1.0000 ISCVel= 0 DCNTRL-CM-options: NTRFrq= 9999999 DCNTRL-heating: IHTFrq= 0 FINAlt= 298.00 IASOrs= 0 TEMInc= 5.00 DCNTRL-equilibration: IEQFrq= 0 ICHEcw= 0 TWINdh= 5.000 TWINdl= -5.000 DCNTRL-langevin: ILBFrq= 0 TBATh= 298.000 RBUF= 0.000 ORIGin=( 0.000000 0.000000 0.000000 ) Verlet algorithm is used. DYNAmics>end ASSFIL: file /home/schwitrs/xplor/test/tracrd.dat opened. ASSFIL: file /home/schwitrs/xplor/test/travel.dat opened. DYNAMC: number of degrees of freedom= 48 ASSVEL: velocities assigned at 1250.0000 K, SEED= 311.000000 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 3.66855 0.78910 -1.36292 velocity [A/ps] : 0.02560 0.62659 9.37282 ang. mom. [amu A/ps] : -1688.70204 -1976.54530 -1242.19753 kin. ener. [Kcal/mol] : 17.42004 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 3.66855 0.78910 -1.36292 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 HBONDS: allocating space for 4 h-bond interactions. HBONDS: 2 distance exclusions and 5 angle exclusions HBONDS: 0 fixed h-bonds, currently 1 h-bonds present --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=-7.139 E(kin)=55.785 temperature=1169.675 | | Etotal =-62.924 grad(E)=12.143 E(BOND)=1.171 E(ANGL)=4.663 | | E(DIHE)=3.599 E(IMPR)=6.918 E(VDW )=-2.173 E(ELEC)=-77.101 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- WRITEC: CORD sets starting from step 2 are written every 2 steps WRITEC: where 2 atoms are "free" WRITEC: VELD sets starting from step 4 are written every 4 steps WRITEC: where 2 atoms are "free" HBONDS: allocating space for 4 h-bond interactions. HBONDS: 2 distance exclusions and 5 angle exclusions HBONDS: 0 fixed h-bonds, currently 1 h-bonds present HBONDS: allocating space for 4 h-bond interactions. HBONDS: 2 distance exclusions and 5 angle exclusions HBONDS: 0 fixed h-bonds, currently 1 h-bonds present HBONDS: allocating space for 4 h-bond interactions. HBONDS: 2 distance exclusions and 4 angle exclusions HBONDS: 0 fixed h-bonds, currently 2 h-bonds present HBONDS: allocating space for 5 h-bond interactions. HBONDS: 2 distance exclusions and 4 angle exclusions HBONDS: 0 fixed h-bonds, currently 2 h-bonds present HBONDS: allocating space for 5 h-bond interactions. HBONDS: 2 distance exclusions and 4 angle exclusions HBONDS: 0 fixed h-bonds, currently 2 h-bonds present HBONDS: allocating space for 5 h-bond interactions. HBONDS: 2 distance exclusions and 5 angle exclusions HBONDS: 0 fixed h-bonds, currently 1 h-bonds present HBONDS: allocating space for 4 h-bond interactions. HBONDS: 2 distance exclusions and 5 angle exclusions HBONDS: 0 fixed h-bonds, currently 1 h-bonds present CENMAS: Information about center of free masses position [A] : 3.69587 0.83003 -1.34567 velocity [A/ps] : 1.26211 0.46605 0.18349 ang. mom. [amu A/ps] : -204.05486 589.28696 122.99925 kin. ener. [Kcal/mol] : 0.36398 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR>dynamics analysis average AVECOR> input=tracrd.dat begin=4 skip=4 stop=60 ASSFIL: file /home/schwitrs/xplor/test/tracrd.dat opened. AVECOR>end REMARKS FILENAME="/home/schwitrs/xplor/test/tracrd.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 2 READC: 2 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 4 SKIP= 4 STOP= 60 READC: TIMEstep= 0.00100000 ps header= CORD READC: complete. 15 coordinate sets were passed to calling routine AVECOR: average set and RMS have been copied to main set. X-PLOR> X-PLOR>close tracrd.dat end X-PLOR> X-PLOR>write coor end REMARK FILENAME="stdout" REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARK AND CG 50 STEPS REMARK EPS=R POTENTIAL REMARK DATE:11-Jun-07 15:21:40 created by user: schwitrs ATOM 1 HT1 TRP 1 0.096 0.610 -1.453 1.00 0.00 TRYP ATOM 2 HT2 TRP 1 1.715 0.532 -1.833 1.00 0.00 TRYP ATOM 3 N TRP 1 1.067 0.302 -1.101 1.00 0.00 TRYP ATOM 4 HT3 TRP 1 1.123 -0.690 -0.828 1.00 0.00 TRYP ATOM 5 CA TRP 1 1.472 1.192 0.027 1.00 0.00 TRYP ATOM 6 CB TRP 1 2.709 1.980 -0.311 1.00 0.07 TRYP ATOM 7 CG TRP 1 3.915 1.141 -0.692 1.00 0.00 TRYP ATOM 8 CD2 TRP 1 4.324 0.683 -1.885 1.00 0.00 TRYP ATOM 9 CE2 TRP 1 5.414 -0.054 -1.622 1.00 0.00 TRYP ATOM 10 CE3 TRP 1 3.761 0.774 -3.141 1.00 0.00 TRYP ATOM 11 CD1 TRP 1 4.805 0.758 0.281 1.00 0.00 TRYP ATOM 12 NE1 TRP 1 5.723 0.069 -0.328 1.00 0.00 TRYP ATOM 13 HE1 TRP 1 6.268 -0.677 0.142 1.00 0.00 TRYP ATOM 14 CZ2 TRP 1 6.153 -0.679 -2.559 1.00 0.00 TRYP ATOM 15 CZ3 TRP 1 4.468 0.118 -4.152 1.00 0.00 TRYP ATOM 16 CH2 TRP 1 5.623 -0.591 -3.830 1.00 0.00 TRYP ATOM 17 C TRP 1 0.280 2.113 0.309 1.00 0.00 TRYP ATOM 18 OT1 TRP 1 -0.455 2.377 -0.641 1.00 0.07 TRYP ATOM 19 OT2 TRP 1 -0.089 2.204 1.445 1.00 0.00 TRYP END X-PLOR> X-PLOR>dynamics analysis average AVECOR> input=travel.dat begin=4 skip=4 stop=60 ASSFIL: file /home/schwitrs/xplor/test/travel.dat opened. AVECOR>end REMARKS FILENAME="/home/schwitrs/xplor/test/travel.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 4 READC: 2 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 4 SKIP= 4 STOP= 60 READC: TIMEstep= 0.00100000 ps header= VELD READC: complete. 15 coordinate sets were passed to calling routine AVECOR: average set and RMS have been copied to main set. X-PLOR> X-PLOR>close travel.dat end X-PLOR>open travel.dat access=append end close travel.dat disp=delete end ASSFIL: file /home/schwitrs/xplor/test/travel.dat opened. X-PLOR> X-PLOR>write coor end REMARK FILENAME="stdout" REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARK AND CG 50 STEPS REMARK EPS=R POTENTIAL REMARK DATE:11-Jun-07 15:21:40 created by user: schwitrs ATOM 1 HT1 TRP 1 1.016 0.430 -0.442 1.00 0.00 TRYP ATOM 2 HT2 TRP 1 0.758 2.162 0.656 1.00 0.00 TRYP ATOM 3 N TRP 1 0.000 0.000 0.000 1.00 0.00 TRYP ATOM 4 HT3 TRP 1 0.756 -0.219 -0.876 1.00 0.00 TRYP ATOM 5 CA TRP 1 0.000 0.000 0.000 1.00 0.00 TRYP ATOM 6 CB TRP 1 -0.410 0.307 0.345 1.00 0.00 TRYP ATOM 7 CG TRP 1 0.071 0.088 0.028 1.00 0.68 TRYP ATOM 8 CD2 TRP 1 0.274 -0.076 -0.059 1.00 0.00 TRYP ATOM 9 CE2 TRP 1 0.070 -0.770 -0.312 1.00 0.00 TRYP ATOM 10 CE3 TRP 1 -0.032 0.003 0.259 1.00 0.00 TRYP ATOM 11 CD1 TRP 1 -0.218 -0.333 -0.181 1.00 0.00 TRYP ATOM 12 NE1 TRP 1 -0.058 0.184 -0.084 1.00 0.00 TRYP ATOM 13 HE1 TRP 1 3.076 4.161 -0.698 1.00 0.00 TRYP ATOM 14 CZ2 TRP 1 0.278 -0.130 -0.021 1.00 0.00 TRYP ATOM 15 CZ3 TRP 1 -0.135 0.239 0.032 1.00 0.00 TRYP ATOM 16 CH2 TRP 1 -0.254 0.337 0.522 1.00 0.00 TRYP ATOM 17 C TRP 1 0.000 0.000 0.000 1.00 0.00 TRYP ATOM 18 OT1 TRP 1 -0.138 -0.147 0.033 1.00 0.20 TRYP ATOM 19 OT2 TRP 1 0.412 0.333 -0.218 1.00 0.00 TRYP END X-PLOR> X-PLOR>{* now test the parsing facility for trajectory reading and writing *} X-PLOR>read trajectory READ-TRAJectory> input=tracrd.dat ASSFIL: file /home/schwitrs/xplor/test/tracrd.dat opened. READ-TRAJectory> begin=4 READ-TRAJectory> skip=4 READ-TRAJectory> stop=60 READ-TRAJectory>end REMARKS FILENAME="/home/schwitrs/xplor/test/tracrd.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 2 READC: 2 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 4 SKIP= 4 STOP= 60 READC: TIMEstep= 0.00100000 ps header= CORD READ-TRAJectory: frame # 4 has been copied to the main coordinate set. X-PLOR>write trajectory WRITe-DYNAmics> output=ttt.dat ascii=false selection=( name ot1 or name cb ) SELRPN: 2 atoms have been selected out of 19 WRITe-DYNAmics>end ASSFIL: file /home/schwitrs/xplor/test/ttt.dat opened. WRITEC: CORD sets starting from step 1 are written every 1 steps WRITEC: where 2 atoms are "free" X-PLOR> X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 8 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 12 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 16 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 20 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 24 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 28 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 32 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 36 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 40 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 44 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 48 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 52 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 56 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READC: complete. 15 coordinate sets were passed to calling routine READCP: trajectory number 60 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as false X-PLOR> read trajectory next end X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR> X-PLOR>close ttt.dat end X-PLOR> X-PLOR>dynamics analysis average AVECOR> ascii=false input=ttt.dat begin=1 skip=1 stop=15 ASSFIL: file /home/schwitrs/xplor/test/ttt.dat opened. AVECOR>end REMARKS FILENAME="/home/schwitrs/xplor/test/ttt.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 1 READC: 2 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 1 SKIP= 1 STOP= 15 READC: TIMEstep= 1.00000000 ps header= CORD READC: complete. 15 coordinate sets were passed to calling routine AVECOR: average set and RMS have been copied to main set. X-PLOR> X-PLOR>write coor end REMARK FILENAME="stdout" REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARK AND CG 50 STEPS REMARK EPS=R POTENTIAL REMARK DATE:11-Jun-07 15:21:40 created by user: schwitrs ATOM 1 HT1 TRP 1 0.096 0.610 -1.453 1.00 0.00 TRYP ATOM 2 HT2 TRP 1 1.715 0.532 -1.833 1.00 0.00 TRYP ATOM 3 N TRP 1 1.067 0.302 -1.101 1.00 0.00 TRYP ATOM 4 HT3 TRP 1 1.123 -0.690 -0.828 1.00 0.00 TRYP ATOM 5 CA TRP 1 1.472 1.192 0.027 1.00 0.00 TRYP ATOM 6 CB TRP 1 2.709 1.980 -0.311 1.00 0.07 TRYP ATOM 7 CG TRP 1 3.915 1.141 -0.692 1.00 0.00 TRYP ATOM 8 CD2 TRP 1 4.324 0.683 -1.885 1.00 0.00 TRYP ATOM 9 CE2 TRP 1 5.414 -0.054 -1.622 1.00 0.00 TRYP ATOM 10 CE3 TRP 1 3.761 0.774 -3.141 1.00 0.00 TRYP ATOM 11 CD1 TRP 1 4.805 0.758 0.281 1.00 0.00 TRYP ATOM 12 NE1 TRP 1 5.723 0.069 -0.328 1.00 0.00 TRYP ATOM 13 HE1 TRP 1 6.268 -0.677 0.142 1.00 0.00 TRYP ATOM 14 CZ2 TRP 1 6.153 -0.679 -2.559 1.00 0.00 TRYP ATOM 15 CZ3 TRP 1 4.468 0.118 -4.152 1.00 0.00 TRYP ATOM 16 CH2 TRP 1 5.623 -0.591 -3.830 1.00 0.00 TRYP ATOM 17 C TRP 1 0.280 2.113 0.309 1.00 0.00 TRYP ATOM 18 OT1 TRP 1 -0.455 2.377 -0.641 1.00 0.07 TRYP ATOM 19 OT2 TRP 1 -0.089 2.204 1.445 1.00 0.00 TRYP END X-PLOR> X-PLOR>{* now test the parsing facility for trajectory reading and writing *} X-PLOR>{* (formatted *} X-PLOR>read trajectory READ-TRAJectory> input=tracrd.dat READ-TRAJectory> begin=4 READ-TRAJectory> skip=4 READ-TRAJectory> stop=60 READ-TRAJectory>end REMARKS FILENAME="/home/schwitrs/xplor/test/tracrd.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 2 READC: 2 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 4 SKIP= 4 STOP= 60 READC: TIMEstep= 0.00100000 ps header= CORD READ-TRAJectory: frame # 4 has been copied to the main coordinate set. X-PLOR>write trajectory WRITe-DYNAmics> reset WRITe-DYNAmics> output=fttt.dat ascii=true selection=( name ot1 or name cb ) SELRPN: 2 atoms have been selected out of 19 WRITe-DYNAmics> format="12Z6" offset=800. scale=10000. WRITe-DYNAmics>end ASSFIL: file /home/schwitrs/xplor/test/fttt.dat opened. WRITEC: CORD sets starting from step 1 are written every 1 steps WRITEC: where 2 atoms are "free" X-PLOR> X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 8 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 12 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 16 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 20 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 24 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 28 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 32 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 36 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 40 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 44 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 48 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 52 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READCP: trajectory number 56 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as true X-PLOR> read trajectory next end READC: complete. 15 coordinate sets were passed to calling routine READCP: trajectory number 60 has been copied to the main coordinate set X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR>while ($status # "COMPLETE" ) loop rrr NEXTCD: condition evaluated as false X-PLOR> read trajectory next end X-PLOR> write trajectory next end X-PLOR>end loop rrr X-PLOR> X-PLOR>close fttt.dat end X-PLOR> X-PLOR>dynamics analysis average AVECOR> ascii=true input=fttt.dat begin=1 skip=1 stop=15 ASSFIL: file /home/schwitrs/xplor/test/fttt.dat opened. AVECOR>end REMARKS FILENAME="/home/schwitrs/xplor/test/fttt.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 1 READC: 2 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 1 SKIP= 1 STOP= 15 READC: TIMEstep= 0.99999856 ps header= CORD READC: complete. 15 coordinate sets were passed to calling routine AVECOR: average set and RMS have been copied to main set. X-PLOR> X-PLOR>write coor end REMARK FILENAME="stdout" REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARK AND CG 50 STEPS REMARK EPS=R POTENTIAL REMARK DATE:11-Jun-07 15:21:40 created by user: schwitrs ATOM 1 HT1 TRP 1 0.096 0.610 -1.453 1.00 0.00 TRYP ATOM 2 HT2 TRP 1 1.715 0.532 -1.833 1.00 0.00 TRYP ATOM 3 N TRP 1 1.067 0.302 -1.101 1.00 0.00 TRYP ATOM 4 HT3 TRP 1 1.123 -0.691 -0.828 1.00 0.00 TRYP ATOM 5 CA TRP 1 1.472 1.192 0.027 1.00 0.00 TRYP ATOM 6 CB TRP 1 2.709 1.980 -0.311 1.00 0.07 TRYP ATOM 7 CG TRP 1 3.915 1.141 -0.692 1.00 0.00 TRYP ATOM 8 CD2 TRP 1 4.324 0.683 -1.885 1.00 0.00 TRYP ATOM 9 CE2 TRP 1 5.413 -0.054 -1.622 1.00 0.00 TRYP ATOM 10 CE3 TRP 1 3.761 0.774 -3.141 1.00 0.00 TRYP ATOM 11 CD1 TRP 1 4.805 0.758 0.281 1.00 0.00 TRYP ATOM 12 NE1 TRP 1 5.723 0.069 -0.328 1.00 0.00 TRYP ATOM 13 HE1 TRP 1 6.268 -0.677 0.142 1.00 0.00 TRYP ATOM 14 CZ2 TRP 1 6.153 -0.679 -2.559 1.00 0.00 TRYP ATOM 15 CZ3 TRP 1 4.468 0.118 -4.152 1.00 0.00 TRYP ATOM 16 CH2 TRP 1 5.623 -0.591 -3.830 1.00 0.00 TRYP ATOM 17 C TRP 1 0.280 2.113 0.309 1.00 0.00 TRYP ATOM 18 OT1 TRP 1 -0.455 2.377 -0.641 1.00 0.07 TRYP ATOM 19 OT2 TRP 1 -0.089 2.204 1.444 1.00 0.00 TRYP END X-PLOR> X-PLOR>set seed=311. end X-PLOR>dynamics langevin DYNAmics> isvfrq=0 DYNAmics> trajectory=traje.dat nsavc=2 ascii=true DYNAmics> velocity=velos.dat nsavv=4 vascii=true DYNAmics> iasvel=maxwell firstt=100 nprint=0 DYNAmics> nstep=60 timestep=0.001 { [ps] } DYNAmics> iprfrq=0 ihtfrq=0 ieqfrq=0 DYNAmics> ? DCNTRL: Langevin-Verlet-integrator NSTEp= 60 TIMEstep= 0.0010000 ps DCNTRL-statistics: IPRFrq= 0 DCNTRL-save-options: NSAVC= 2 NSAVV= 4 ISVFrq= 0 NPRInt= 0 DCNTRL-V-assignment: FIRStt= 100.000 IASVel=MAXW DCNTRL-V-scaling: ISCFrq= 0 HEAT= 1.0000 ISCVel= 0 DCNTRL-CM-options: NTRFrq= 9999999 DCNTRL-heating: IHTFrq= 0 FINAlt= 298.00 IASOrs= 0 TEMInc= 5.00 DCNTRL-equilibration: IEQFrq= 0 ICHEcw= 0 TWINdh= 5.000 TWINdl= -5.000 DCNTRL-langevin: ILBFrq= 0 TBATh= 298.000 RBUF= 0.000 ORIGin=( 0.000000 0.000000 0.000000 ) Verlet algorithm is used. DYNAmics>end ASSFIL: file /home/schwitrs/xplor/test/traje.dat opened. ASSFIL: file /home/schwitrs/xplor/test/velos.dat opened. DYNAMC: number of degrees of freedom= 48 ASSVEL: velocities assigned at 100.0000 K, SEED= 311.000000 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 3.66671 0.77484 -1.36193 velocity [A/ps] : 0.00724 0.17723 2.65103 ang. mom. [amu A/ps] : -476.74681 -561.94392 -352.37254 kin. ener. [Kcal/mol] : 1.39360 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 3.66671 0.77484 -1.36193 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 HBONDS: allocating space for 4 h-bond interactions. HBONDS: 2 distance exclusions and 5 angle exclusions HBONDS: 0 fixed h-bonds, currently 1 h-bonds present --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=-50.316 E(kin)=4.456 temperature=93.442 | | Etotal =-54.773 grad(E)=26.812 E(BOND)=5.134 E(ANGL)=7.390 | | E(DIHE)=3.597 E(IMPR)=9.786 E(VDW )=-1.475 E(ELEC)=-79.204 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- WRITEC: CORD sets starting from step 2 are written every 2 steps WRITEC: where 16 atoms are "free" WRITEC: VELD sets starting from step 4 are written every 4 steps WRITEC: where 16 atoms are "free" HBONDS: allocating space for 4 h-bond interactions. HBONDS: 2 distance exclusions and 4 angle exclusions HBONDS: 0 fixed h-bonds, currently 2 h-bonds present CENMAS: Information about center of free masses position [A] : 3.70302 0.82887 -1.36301 velocity [A/ps] : 0.55303 0.34412 -0.54560 ang. mom. [amu A/ps] : -260.30290 -121.82421 10.48660 kin. ener. [Kcal/mol] : 0.14252 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR>read dynamics READ-TRAJectory> ascii=true input=traje.dat begin=2 skip=2 stop=60 ASSFIL: file /home/schwitrs/xplor/test/traje.dat opened. READ-TRAJectory>end REMARKS FILENAME="/home/schwitrs/xplor/test/traje.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 2 READC: 16 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 2 SKIP= 2 STOP= 60 READC: TIMEstep= 0.00100000 ps header= CORD READ-TRAJectory: frame # 2 has been copied to the main coordinate set. X-PLOR> X-PLOR>write coordinates end REMARK FILENAME="stdout" REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARK AND CG 50 STEPS REMARK EPS=R POTENTIAL REMARK DATE:11-Jun-07 15:21:40 created by user: schwitrs ATOM 1 HT1 TRP 1 0.110 0.615 -1.457 1.00 0.00 TRYP ATOM 2 HT2 TRP 1 1.727 0.557 -1.828 1.00 0.00 TRYP ATOM 3 N TRP 1 1.067 0.302 -1.101 1.00 0.00 TRYP ATOM 4 HT3 TRP 1 1.132 -0.694 -0.838 1.00 0.00 TRYP ATOM 5 CA TRP 1 1.472 1.192 0.027 1.00 0.00 TRYP ATOM 6 CB TRP 1 2.701 1.986 -0.306 1.00 0.07 TRYP ATOM 7 CG TRP 1 3.915 1.134 -0.693 1.00 0.00 TRYP ATOM 8 CD2 TRP 1 4.327 0.682 -1.886 1.00 0.00 TRYP ATOM 9 CE2 TRP 1 5.414 -0.063 -1.626 1.00 0.00 TRYP ATOM 10 CE3 TRP 1 3.761 0.774 -3.138 1.00 0.00 TRYP ATOM 11 CD1 TRP 1 4.803 0.754 0.279 1.00 0.00 TRYP ATOM 12 NE1 TRP 1 5.722 0.071 -0.329 1.00 0.00 TRYP ATOM 13 HE1 TRP 1 6.301 -0.627 0.133 1.00 0.00 TRYP ATOM 14 CZ2 TRP 1 6.156 -0.681 -2.559 1.00 0.00 TRYP ATOM 15 CZ3 TRP 1 4.466 0.121 -4.152 1.00 0.00 TRYP ATOM 16 CH2 TRP 1 5.620 -0.587 -3.823 1.00 0.00 TRYP ATOM 17 C TRP 1 0.280 2.113 0.309 1.00 0.00 TRYP ATOM 18 OT1 TRP 1 -0.455 2.373 -0.640 1.00 0.07 TRYP ATOM 19 OT2 TRP 1 -0.084 2.208 1.442 1.00 0.00 TRYP END X-PLOR> X-PLOR>read dynamics READ-TRAJectory> ascii=true input=velos.dat begin=16 skip=16 stop=60 ASSFIL: file /home/schwitrs/xplor/test/velos.dat opened. READ-TRAJectory>end REMARKS FILENAME="/home/schwitrs/xplor/test/velos.dat" REMARKS TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARKS AND CG 50 STEPS REMARKS EPS=R POTENTIAL REMARKS DATE:11-Jun-07 15:21:40 created by user: schwitrs READC: reading file= 1 ISTART= 4 READC: 16 atoms were "free" READC: STOP not compatible. Modified READC: NUNIt= 1 READC: BEGIn= 16 SKIP= 16 STOP= 48 READC: TIMEstep= 0.00100000 ps header= VELD READ-TRAJectory: frame # 16 has been copied to the main coordinate set. X-PLOR> X-PLOR>write coordinates end REMARK FILENAME="stdout" REMARK TRYPTOPHAN BUILT AND MINIMIZED WITH SD 50 STEPS, ABNR 500 STEP, REMARK AND CG 50 STEPS REMARK EPS=R POTENTIAL REMARK DATE:11-Jun-07 15:21:40 created by user: schwitrs ATOM 1 HT1 TRP 1 0.291 0.040 0.625 1.00 0.00 TRYP ATOM 2 HT2 TRP 1 -1.061 -0.405 -0.868 1.00 0.00 TRYP ATOM 3 N TRP 1 0.000 0.000 0.000 1.00 0.00 TRYP ATOM 4 HT3 TRP 1 -0.353 0.121 0.520 1.00 0.00 TRYP ATOM 5 CA TRP 1 0.000 0.000 0.000 1.00 0.00 TRYP ATOM 6 CB TRP 1 0.163 0.085 -0.134 1.00 0.07 TRYP ATOM 7 CG TRP 1 -0.173 -0.058 0.033 1.00 0.00 TRYP ATOM 8 CD2 TRP 1 0.160 0.245 0.316 1.00 0.00 TRYP ATOM 9 CE2 TRP 1 -0.344 -0.096 -0.074 1.00 0.00 TRYP ATOM 10 CE3 TRP 1 -0.121 -0.050 -0.056 1.00 0.00 TRYP ATOM 11 CD1 TRP 1 0.047 -0.052 0.286 1.00 0.00 TRYP ATOM 12 NE1 TRP 1 0.090 -0.022 0.361 1.00 0.00 TRYP ATOM 13 HE1 TRP 1 0.796 1.517 -0.379 1.00 0.00 TRYP ATOM 14 CZ2 TRP 1 -0.062 0.111 -0.184 1.00 0.00 TRYP ATOM 15 CZ3 TRP 1 0.224 -0.038 -0.170 1.00 0.00 TRYP ATOM 16 CH2 TRP 1 0.008 -0.132 -0.350 1.00 0.00 TRYP ATOM 17 C TRP 1 0.000 0.000 0.000 1.00 0.00 TRYP ATOM 18 OT1 TRP 1 0.101 0.160 -0.081 1.00 0.07 TRYP ATOM 19 OT2 TRP 1 0.232 0.311 0.229 1.00 0.00 TRYP END X-PLOR>stop HEAP: maximum use= 631006 current use= 610642 X-PLOR: total CPU time= 0.0600 s X-PLOR: entry time at 15:21:40 11-Jun-07 X-PLOR: exit time at 15:21:40 11-Jun-07