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 15:28:47 X-PLOR>remarks POWETEST.INP X-PLOR>remarks TEST power spectrum routine X-PLOR>remarks by Axel Brunger 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> X-PLOR>set seed=311 end X-PLOR>dynamics verlet DYNAmics> isvfrq=0 isvfrq=10 velocity=vpowe.dat nsavv=1 DYNAmics> nstep=100 timestep=0.001 { [ps] } DYNAmics> nprint=0 iprfrq=0 DYNAmics> iasvel=maxwell firstt=1250.0 DYNAmics> ihtfrq=0 ieqfrq=0 DYNAmics>end ASSFIL: file /home/schwitrs/xplor/test/vpowe.dat opened. DYNAMC: number of degrees of freedom= 57 ASSVEL: velocities assigned at 1250.0000 K, SEED= 311.000000 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 3.15083 0.85925 -1.15799 velocity [A/ps] : 2.18847 1.92191 7.09379 ang. mom. [amu A/ps] : 71.96592 -1186.91482 -1303.56586 kin. ener. [Kcal/mol] : 14.35191 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 3.15083 0.85925 -1.15799 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 83 exclusions, 20 interactions(1-4) and 63 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)=8.395 E(kin)=70.147 temperature=1238.582 | | Etotal =-61.752 grad(E)=13.425 E(BOND)=2.002 E(ANGL)=5.003 | | E(DIHE)=3.599 E(IMPR)=6.918 E(VDW )=-2.173 E(ELEC)=-77.101 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- WRITEC: VELD sets starting from step 1 are written every 1 steps WRITEC: where 19 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 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 6 angle exclusions HBONDS: 0 fixed h-bonds, currently 0 h-bonds present HBONDS: allocating space for 8 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 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] : 3.15083 0.85925 -1.15799 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 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR>close vpowe.dat end %X-PLOR>-ERR: File vpowe.dat was not open. X-PLOR> X-PLOR>dynamics analyse powerspectrum POWER> input=vpowe.dat begin=1 skip=1 stop=100 ASSFIL: file /home/schwitrs/xplor/test/vpowe.dat opened. POWER> species=( name CA ) SELRPN: 1 atoms have been selected out of 19 POWER> POUTPUT=OUTPUT pskip=1 plength=500.0 {* ps-1 *} POWER> back=true COUTPUT=OUTPUT clength=1.0 {* ps *} POWER>end POWER: PSKIp= 1 PLENgth= 0.50000E+03 BACK=T TRIM=F POWER: CLENgth= 1.00000 REMARKS FILENAME="/home/schwitrs/xplor/test/vpowe.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 15:28:47 created by user: schwitrs READC: reading file= 1 ISTART= 1 READC: 19 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 1 SKIP= 1 STOP= 100 READC: TIMEstep= 0.00100000 ps header= VELD READC: complete. 100 coordinate sets were passed to calling routine POWER: points in time series= 100, in FFT (padded with zeros)= 128 FFTAC: maximum in spectrum 0.76005E+03 POWER: power spectrum being written (by FFT) 0.00000E+00 0.63004E-32 0.49087E+02 0.10094E+00 0.98175E+02 0.23644E+00 0.14726E+03 0.33707E+00 0.19635E+03 0.99192E+00 0.24544E+03 0.10000E+01 0.29452E+03 0.24770E+00 0.34361E+03 0.11441E+00 0.39270E+03 0.40439E-01 0.44179E+03 0.14080E-01 0.49087E+03 0.69301E-02 BFFTAC: initial value of correlation funct= 0.49453E-01 POWER: correlation function being written 0.00000E+00 0.10000E+01 0.10000E-02 0.95877E+00 0.20000E-02 0.87546E+00 0.30000E-02 0.75547E+00 0.40000E-02 0.60614E+00 0.50000E-02 0.43625E+00 0.60000E-02 0.25541E+00 0.70000E-02 0.73448E-01 0.80000E-02 -0.10023E+00 0.90000E-02 -0.25714E+00 0.10000E-01 -0.39023E+00 0.11000E-01 -0.49420E+00 0.12000E-01 -0.56572E+00 0.13000E-01 -0.60350E+00 0.14000E-01 -0.60825E+00 0.15000E-01 -0.58247E+00 0.16000E-01 -0.53019E+00 0.17000E-01 -0.45655E+00 0.18000E-01 -0.36743E+00 0.19000E-01 -0.26900E+00 0.20000E-01 -0.16735E+00 0.21000E-01 -0.68114E-01 0.22000E-01 0.23819E-01 0.23000E-01 0.10449E+00 0.24000E-01 0.17101E+00 0.25000E-01 0.22158E+00 0.26000E-01 0.25547E+00 0.27000E-01 0.27296E+00 0.28000E-01 0.27512E+00 0.29000E-01 0.26399E+00 0.30000E-01 0.23887E+00 0.31000E-01 0.20224E+00 0.32000E-01 0.15699E+00 0.33000E-01 0.10618E+00 0.34000E-01 0.52917E-01 0.35000E-01 0.20524E-03 0.36000E-01 -0.49230E-01 0.37000E-01 -0.93038E-01 0.38000E-01 -0.12935E+00 0.39000E-01 -0.15682E+00 0.40000E-01 -0.17470E+00 0.41000E-01 -0.18275E+00 0.42000E-01 -0.18133E+00 0.43000E-01 -0.17126E+00 0.44000E-01 -0.15378E+00 0.45000E-01 -0.13047E+00 0.46000E-01 -0.10313E+00 0.47000E-01 -0.73657E-01 0.48000E-01 -0.43936E-01 0.49000E-01 -0.15718E-01 0.50000E-01 0.94710E-02 0.51000E-01 0.30422E-01 0.52000E-01 0.46297E-01 0.53000E-01 0.56664E-01 0.54000E-01 0.61498E-01 0.55000E-01 0.61162E-01 0.56000E-01 0.56356E-01 0.57000E-01 0.48048E-01 0.58000E-01 0.37399E-01 0.59000E-01 0.25664E-01 0.60000E-01 0.14101E-01 0.61000E-01 0.38650E-02 0.62000E-01 -0.40814E-02 0.63000E-01 -0.90430E-02 POWER: integral over correlation function= 0.00013 ps. X-PLOR> X-PLOR> X-PLOR>dynamics analyse powerspectrum POWER> input=vpowe.dat begin=1 skip=1 stop=100 POWER> species=( name CA ) SELRPN: 1 atoms have been selected out of 19 POWER> window=( 0.0 100.0 ) POWER> POUTPUT=OUTPUT pskip=1 plength=500.0 {* ps-1 *} POWER> back=true COUTPUT=OUTPUT clength=1.0 {* ps *} POWER>end POWER: PSKIp= 1 PLENgth= 0.50000E+03 BACK=T TRIM=F POWER: WINDow=( 0.00000 100.00000 ) POWER: CLENgth= 1.00000 REMARKS FILENAME="/home/schwitrs/xplor/test/vpowe.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 15:28:47 created by user: schwitrs READC: reading file= 1 ISTART= 1 READC: 19 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 1 SKIP= 1 STOP= 100 READC: TIMEstep= 0.00100000 ps header= VELD READC: complete. 100 coordinate sets were passed to calling routine POWER: points in time series= 100, in FFT (padded with zeros)= 128 FFTAC: maximum in spectrum 0.76005E+03 POWER: power spectrum being written (by FFT) 0.00000E+00 0.00000E+00 0.49087E+02 0.10094E+00 0.98175E+02 0.23644E+00 0.14726E+03 0.00000E+00 0.19635E+03 0.00000E+00 0.24544E+03 0.00000E+00 0.29452E+03 0.00000E+00 0.34361E+03 0.00000E+00 0.39270E+03 0.00000E+00 0.44179E+03 0.00000E+00 0.49087E+03 0.00000E+00 BFFTAC: initial value of correlation funct= 0.26358E-02 POWER: correlation function being written 0.00000E+00 0.10000E+01 0.10000E-02 0.99407E+00 0.20000E-02 0.98072E+00 0.30000E-02 0.96009E+00 0.40000E-02 0.93241E+00 0.50000E-02 0.89794E+00 0.60000E-02 0.85704E+00 0.70000E-02 0.81009E+00 0.80000E-02 0.75755E+00 0.90000E-02 0.69991E+00 0.10000E-01 0.63771E+00 0.11000E-01 0.57153E+00 0.12000E-01 0.50198E+00 0.13000E-01 0.42970E+00 0.14000E-01 0.35534E+00 0.15000E-01 0.27958E+00 0.16000E-01 0.20309E+00 0.17000E-01 0.12656E+00 0.18000E-01 0.50645E-01 0.19000E-01 -0.23983E-01 0.20000E-01 -0.96687E-01 0.21000E-01 -0.16685E+00 0.22000E-01 -0.23389E+00 0.23000E-01 -0.29725E+00 0.24000E-01 -0.35644E+00 0.25000E-01 -0.41098E+00 0.26000E-01 -0.46047E+00 0.27000E-01 -0.50455E+00 0.28000E-01 -0.54292E+00 0.29000E-01 -0.57534E+00 0.30000E-01 -0.60162E+00 0.31000E-01 -0.62167E+00 0.32000E-01 -0.63541E+00 0.33000E-01 -0.64286E+00 0.34000E-01 -0.64409E+00 0.35000E-01 -0.63924E+00 0.36000E-01 -0.62850E+00 0.37000E-01 -0.61212E+00 0.38000E-01 -0.59040E+00 0.39000E-01 -0.56369E+00 0.40000E-01 -0.53240E+00 0.41000E-01 -0.49697E+00 0.42000E-01 -0.45786E+00 0.43000E-01 -0.41559E+00 0.44000E-01 -0.37069E+00 0.45000E-01 -0.32372E+00 0.46000E-01 -0.27523E+00 0.47000E-01 -0.22581E+00 0.48000E-01 -0.17601E+00 0.49000E-01 -0.12642E+00 0.50000E-01 -0.77578E-01 0.51000E-01 -0.30031E-01 0.52000E-01 0.15708E-01 0.53000E-01 0.59154E-01 0.54000E-01 0.99856E-01 0.55000E-01 0.13740E+00 0.56000E-01 0.17142E+00 0.57000E-01 0.20159E+00 0.58000E-01 0.22764E+00 0.59000E-01 0.24936E+00 0.60000E-01 0.26657E+00 0.61000E-01 0.27918E+00 0.62000E-01 0.28713E+00 0.63000E-01 0.29044E+00 POWER: integral over correlation function= 0.00033 ps. X-PLOR> X-PLOR>close vpowe.dat end X-PLOR>open vpowe.dat access=append end close vpowe.dat disp=delete end ASSFIL: file /home/schwitrs/xplor/test/vpowe.dat opened. X-PLOR> X-PLOR>stop HEAP: maximum use= 631006 current use= 610470 X-PLOR: total CPU time= 0.0400 s X-PLOR: entry time at 15:28:47 11-Jun-07 X-PLOR: exit time at 15:28:48 11-Jun-07