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 15:23:30 X-PLOR>remarks PICKTEST.INP X-PLOR>remarks TEST PICKING OF GEOMETRIC PROPERTIES 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> 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>set wrnlev=4 end X-PLOR> X-PLOR>coor copy end 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>{* just print bonds, angles,... *} X-PLOR>{* ============================ *} X-PLOR>print bonds (atom-i |atom-j ) dist. equil. delta energy const. (TRYP 1 N |TRYP 1 CA ) 1.493 1.450 0.043 0.766 422.000 (TRYP 1 CA |TRYP 1 C ) 1.533 1.520 0.013 0.065 405.000 (TRYP 1 CA |TRYP 1 CB ) 1.528 1.520 0.008 0.013 225.000 (TRYP 1 CB |TRYP 1 CG ) 1.532 1.520 0.012 0.062 405.000 (TRYP 1 CG |TRYP 1 CD1 ) 1.374 1.380 -0.006 0.016 450.000 (TRYP 1 CG |TRYP 1 CD2 ) 1.359 1.380 -0.021 0.198 450.000 (TRYP 1 CD1 |TRYP 1 NE1 ) 1.319 1.305 0.014 0.090 450.000 (TRYP 1 CD2 |TRYP 1 CE2 ) 1.354 1.380 -0.026 0.306 450.000 (TRYP 1 NE1 |TRYP 1 HE1 ) 0.979 0.980 -0.001 0.001 405.000 (TRYP 1 NE1 |TRYP 1 CE2 ) 1.317 1.330 -0.013 0.076 471.000 (TRYP 1 CD2 |TRYP 1 CE3 ) 1.373 1.380 -0.007 0.023 450.000 (TRYP 1 CE2 |TRYP 1 CZ2 ) 1.371 1.380 -0.009 0.039 450.000 (TRYP 1 CE3 |TRYP 1 CZ3 ) 1.387 1.380 0.007 0.022 450.000 (TRYP 1 CZ2 |TRYP 1 CH2 ) 1.389 1.380 0.009 0.039 450.000 (TRYP 1 CZ3 |TRYP 1 CH2 ) 1.396 1.380 0.016 0.121 450.000 (TRYP 1 HT1 |TRYP 1 N ) 1.043 1.040 0.003 0.004 405.000 (TRYP 1 HT2 |TRYP 1 N ) 1.039 1.040 -0.001 0.001 405.000 (TRYP 1 HT3 |TRYP 1 N ) 1.039 1.040 -0.001 0.001 405.000 (TRYP 1 C |TRYP 1 OT1 ) 1.222 1.230 -0.008 0.036 580.000 (TRYP 1 C |TRYP 1 OT2 ) 1.215 1.230 -0.015 0.122 580.000 RMS deviation= 0.015 X-PLOR>display $rms $violations 1.50619E-02 20 X-PLOR>print angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. (TRYP 1 N |TRYP 1 CA |TRYP 1 C ) 106.619 111.600 -4.981 0.340 45.000 (TRYP 1 N |TRYP 1 CA |TRYP 1 CB ) 110.940 110.000 0.940 0.017 65.000 (TRYP 1 C |TRYP 1 CA |TRYP 1 CB ) 109.874 109.500 0.374 0.003 70.000 (TRYP 1 CA |TRYP 1 CB |TRYP 1 CG ) 112.850 112.500 0.350 0.003 70.000 (TRYP 1 CB |TRYP 1 CG |TRYP 1 CD1 ) 121.772 121.500 0.272 0.002 70.000 (TRYP 1 CB |TRYP 1 CG |TRYP 1 CD2 ) 127.897 126.500 1.397 0.039 65.000 (TRYP 1 CD1 |TRYP 1 CG |TRYP 1 CD2 ) 110.327 122.500 -12.173 3.160 70.000 (TRYP 1 CG |TRYP 1 CD1 |TRYP 1 NE1 ) 106.343 109.500 -3.157 0.273 90.000 (TRYP 1 CG |TRYP 1 CD2 |TRYP 1 CE2 ) 102.821 106.500 -3.679 0.289 70.000 (TRYP 1 CD1 |TRYP 1 NE1 |TRYP 1 HE1 ) 119.630 120.000 -0.370 0.001 35.000 (TRYP 1 CD1 |TRYP 1 NE1 |TRYP 1 CE2 ) 108.303 108.000 0.303 0.002 60.000 (TRYP 1 CD2 |TRYP 1 CE2 |TRYP 1 NE1 ) 112.206 109.000 3.206 0.203 65.000 (TRYP 1 CE2 |TRYP 1 CD2 |TRYP 1 CE3 ) 123.482 122.500 0.982 0.021 70.000 (TRYP 1 CD2 |TRYP 1 CE2 |TRYP 1 CZ2 ) 122.119 122.500 -0.381 0.003 70.000 (TRYP 1 HE1 |TRYP 1 NE1 |TRYP 1 CE2 ) 119.718 120.000 -0.282 0.001 30.000 (TRYP 1 CD2 |TRYP 1 CE3 |TRYP 1 CZ3 ) 115.606 119.000 -3.394 0.316 90.000 (TRYP 1 CE2 |TRYP 1 CZ2 |TRYP 1 CH2 ) 116.131 119.000 -2.869 0.226 90.000 (TRYP 1 CE3 |TRYP 1 CZ3 |TRYP 1 CH2 ) 121.209 120.500 0.709 0.014 90.000 (TRYP 1 CZ2 |TRYP 1 CH2 |TRYP 1 CZ3 ) 121.453 120.500 0.953 0.025 90.000 (TRYP 1 HT1 |TRYP 1 N |TRYP 1 HT2 ) 109.238 109.500 -0.262 0.001 40.000 (TRYP 1 HT2 |TRYP 1 N |TRYP 1 HT3 ) 110.287 109.500 0.787 0.008 40.000 (TRYP 1 HT2 |TRYP 1 N |TRYP 1 CA ) 109.853 109.500 0.353 0.001 35.000 (TRYP 1 HT1 |TRYP 1 N |TRYP 1 HT3 ) 109.976 109.500 0.476 0.003 40.000 (TRYP 1 HT1 |TRYP 1 N |TRYP 1 CA ) 107.582 109.500 -1.918 0.039 35.000 (TRYP 1 HT3 |TRYP 1 N |TRYP 1 CA ) 109.859 109.500 0.359 0.001 35.000 (TRYP 1 CA |TRYP 1 C |TRYP 1 OT1 ) 118.215 117.500 0.715 0.013 85.000 (TRYP 1 CA |TRYP 1 C |TRYP 1 OT2 ) 117.374 117.500 -0.126 0.000 85.000 (TRYP 1 OT1 |TRYP 1 C |TRYP 1 OT2 ) 122.346 122.500 -0.154 0.001 85.000 RMS deviation= 2.915 X-PLOR>display $rms $violations 2.91497 28 X-PLOR>print dihedrals (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period (TRYP 1 N |TRYP 1 CA |TRYP 1 CB |TRYP 1 CG ) -60.893 -60.000 0.893 0.002 1.600 3 (TRYP 1 CA |TRYP 1 CB |TRYP 1 CG |TRYP 1 CD1 ) -88.927 -60.000 28.927 0.000 0.000 3 (TRYP 1 CD1 |TRYP 1 CE2 |TRYP 1 CD2 |TRYP 1 CZ3 ) 179.999 180.000 0.001 0.000 5.000 2 (TRYP 1 CD1 |TRYP 1 CD2 |TRYP 1 CE2 |TRYP 1 CH2 ) 179.997 180.000 0.003 0.000 5.000 2 (TRYP 1 CZ2 |TRYP 1 CE2 |TRYP 1 CD2 |TRYP 1 CG ) 179.938 180.000 0.062 0.000 2.500 2 (TRYP 1 CE3 |TRYP 1 CD2 |TRYP 1 CE2 |TRYP 1 NE1 ) -179.994 -180.000 -0.006 0.000 2.500 2 (TRYP 1 HT2 |TRYP 1 N |TRYP 1 CA |TRYP 1 C ) 119.939 60.000 -59.939 1.200 0.600 3 (TRYP 1 HT1 |TRYP 1 N |TRYP 1 CA |TRYP 1 C ) 1.130 60.000 58.870 1.199 0.600 3 (TRYP 1 HT3 |TRYP 1 N |TRYP 1 CA |TRYP 1 C ) -118.571 -60.000 58.571 1.198 0.600 3 (TRYP 1 N |TRYP 1 CA |TRYP 1 C |TRYP 1 OT2 ) 129.072 180.000 50.928 0.000 0.000 3 RMS deviation= 37.310 X-PLOR>display $rms $violations 37.3098 10 X-PLOR>print impropers (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period (TRYP 1 CA |TRYP 1 N |TRYP 1 C |TRYP 1 CB ) 34.643 35.264 0.621 0.006 55.000 0 (TRYP 1 CG |TRYP 1 CD1 |TRYP 1 CD2 |TRYP 1 CB ) -0.377 0.000 0.377 0.004 90.000 0 (TRYP 1 NE1 |TRYP 1 CD1 |TRYP 1 CE2 |TRYP 1 HE1 ) 18.104 0.000 -18.104 4.493 45.000 0 (TRYP 1 CD2 |TRYP 1 CE2 |TRYP 1 CZ2 |TRYP 1 CH2 ) 0.011 0.000 -0.011 0.000 25.000 0 (TRYP 1 CE2 |TRYP 1 CZ2 |TRYP 1 CH2 |TRYP 1 CZ3 ) -0.002 0.000 0.002 0.000 25.000 0 (TRYP 1 CZ2 |TRYP 1 CH2 |TRYP 1 CZ3 |TRYP 1 CE3 ) 0.002 0.000 -0.002 0.000 25.000 0 (TRYP 1 CH2 |TRYP 1 CZ3 |TRYP 1 CE3 |TRYP 1 CD2 ) -0.010 0.000 0.010 0.000 25.000 0 (TRYP 1 CZ3 |TRYP 1 CE3 |TRYP 1 CD2 |TRYP 1 CE2 ) 0.019 0.000 -0.019 0.000 25.000 0 (TRYP 1 CE3 |TRYP 1 CD2 |TRYP 1 CE2 |TRYP 1 CZ2 ) -0.021 0.000 0.021 0.000 25.000 0 (TRYP 1 CG |TRYP 1 CD1 |TRYP 1 NE1 |TRYP 1 CE2 ) 0.080 0.000 -0.080 0.000 25.000 0 (TRYP 1 CD1 |TRYP 1 NE1 |TRYP 1 CE2 |TRYP 1 CD2 ) -0.030 0.000 0.030 0.000 25.000 0 (TRYP 1 NE1 |TRYP 1 CE2 |TRYP 1 CD2 |TRYP 1 CG ) -0.035 0.000 0.035 0.000 100.000 0 (TRYP 1 CE2 |TRYP 1 CD2 |TRYP 1 CG |TRYP 1 CD1 ) 0.084 0.000 -0.084 0.000 25.000 0 (TRYP 1 CD2 |TRYP 1 CG |TRYP 1 CD1 |TRYP 1 NE1 ) -0.105 0.000 0.105 0.000 100.000 0 (TRYP 1 C |TRYP 1 CA |TRYP 1 OT2 |TRYP 1 OT1 ) 8.903 0.000 -8.903 2.415 100.000 0 RMS deviation= 5.213 X-PLOR>display $rms $violations 5.21257 15 X-PLOR> X-PLOR>print threshold=0.1 bonds (atom-i |atom-j ) dist. equil. delta energy const. Number of violations greater 0.100: 0 RMS deviation= 0.015 X-PLOR>display $rms $violations 1.50619E-02 0 X-PLOR>print threshold=10.0 angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. (TRYP 1 CD1 |TRYP 1 CG |TRYP 1 CD2 ) 110.327 122.500 -12.173 3.160 70.000 Number of violations greater 10.000: 1 RMS deviation= 2.915 X-PLOR>display $rms $violations 2.91497 1 X-PLOR>print threshold=40.0 dihedrals (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period (TRYP 1 HT2 |TRYP 1 N |TRYP 1 CA |TRYP 1 C ) 119.939 60.000 -59.939 1.200 0.600 3 (TRYP 1 HT1 |TRYP 1 N |TRYP 1 CA |TRYP 1 C ) 1.130 60.000 58.870 1.199 0.600 3 (TRYP 1 HT3 |TRYP 1 N |TRYP 1 CA |TRYP 1 C ) -118.571 -60.000 58.571 1.198 0.600 3 (TRYP 1 N |TRYP 1 CA |TRYP 1 C |TRYP 1 OT2 ) 129.072 180.000 50.928 0.000 0.000 3 Number of violations greater 40.000: 4 RMS deviation= 37.310 X-PLOR>display $rms $violations 37.3098 4 X-PLOR>print threshold=20.0 impropers (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period Number of violations greater 20.000: 0 RMS deviation= 5.213 X-PLOR>display $rms $violations 5.21257 0 X-PLOR> X-PLOR> X-PLOR>{* test individual picking *} X-PLOR>{* ======================= *} X-PLOR>pick bond ( atom tryp 1 ca ) ( atom tryp 1 cb ) geometry X-PLOR>display $result 1.52757 X-PLOR>pick bond ( atom tryp 1 ca ) ( atom tryp 1 cb ) energy X-PLOR>display $result 1.289768E-02 X-PLOR>pick bond ( atom tryp 1 ca ) ( atom tryp 1 cb ) equilibrium X-PLOR>display $result 1.52 X-PLOR>pick bond ( atom tryp 1 ca ) ( atom tryp 1 cb ) delta X-PLOR>display $result 7.571197E-03 X-PLOR>pick bond ( atom tryp 1 ca ) ( atom tryp 1 cb ) constant X-PLOR>display $result 225 X-PLOR>pick bond ( atom tryp 1 c* ) ( atom tryp 1 n* ) geometry X-PLOR>display $result 1.15349 X-PLOR> X-PLOR>pick angle ( atom tryp 1 ca ) ( atom tryp 1 cb ) ( atom tryp 1 cg ) geometry X-PLOR>display $result 112.85 X-PLOR> X-PLOR>pick dihedral SELRPN> (atom tryp 1 n) (atom tryp 1 ca) (atom tryp 1 cb) (atom tryp 1 cg) geometry X-PLOR>display $result -60.8926 X-PLOR>pick dihedral SELRPN> (atom tryp 1 n) (atom tryp 1 ca) (atom tryp 1 cb) (atom tryp 1 cg) energy X-PLOR>display $result 1.747129E-03 X-PLOR> X-PLOR>pick improper SELRPN> (atom tryp 1 ca) (atom tryp 1 n) (atom tryp 1 c) (atom tryp 1 cb) geometry X-PLOR>display $result 34.6432 X-PLOR>pick improper SELRPN> (atom tryp 1 ca) (atom tryp 1 n) (atom tryp 1 c) (atom tryp 1 cb) energy X-PLOR>display $result 6.464435E-03 X-PLOR> X-PLOR>pick ring SELRPN> (name ca)(name cb)(name cg)(name cd2)(name c) pucker PUCKer= 0.691746 13.425201 X-PLOR>display $n_amplitude $n_phase 1 1 X-PLOR>display $amplitude1 $phase1 0.691746 13.4252 X-PLOR> X-PLOR>pick ring SELRPN> (name ca)(name cb)(name cg)(name cd2)(name c) (name n ) pucker PUCKer= 1.160614 -0.258721 66.922853 X-PLOR>display $n_amplitude $n_phase 2 1 X-PLOR>display $amplitude1 $phase1 1.16061 66.9229 X-PLOR>display $amplitude2 -0.258721 X-PLOR> X-PLOR> X-PLOR>{* test the generation of time series of geometric properties *} X-PLOR>{* ========================================================== *} X-PLOR>set seed=311. end X-PLOR>dynamics langevin DYNAmics> isvfrq=0 trajectory=pick1.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>end 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 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: CORD sets starting from step 2 are written every 2 steps WRITEC: where 19 atoms are "free" --------------- step= 10 at 0.01000 ps -------------------------------- | E(kin)+E(total)=8.646 E(kin)=48.993 temperature=865.062 | | Etotal =-40.346 grad(E)=30.710 E(BOND)=8.587 E(ANGL)=15.377 | | E(DIHE)=3.925 E(IMPR)=11.067 E(VDW )=-0.940 E(ELEC)=-78.362 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- averages for last 10 steps ----------------------------- | E(kin)+E(total)=8.942 E(kin)=42.867 temperature=756.899 | | Etotal =-33.925 grad(E)=39.302 E(BOND)=15.656 E(ANGL)=14.514 | | E(DIHE)=3.668 E(IMPR)=12.363 E(VDW )=-1.503 E(ELEC)=-78.622 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 10 steps ----------------------- | E(kin)+E(total)=0.212 E(kin)=11.861 temperature=209.425 | | Etotal =12.048 grad(E)=8.772 E(BOND)=5.849 E(ANGL)=3.896 | | E(DIHE)=0.134 E(IMPR)=2.880 E(VDW )=0.583 E(ELEC)=0.366 | | 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)=8.718 E(kin)=48.060 temperature=848.591 | | Etotal =-39.341 grad(E)=35.539 E(BOND)=7.983 E(ANGL)=16.438 | | E(DIHE)=4.079 E(IMPR)=11.042 E(VDW )=-2.360 E(ELEC)=-76.523 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- averages for last 10 steps ----------------------------- | E(kin)+E(total)=8.870 E(kin)=46.628 temperature=823.316 | | Etotal =-37.758 grad(E)=38.649 E(BOND)=9.173 E(ANGL)=20.898 | | E(DIHE)=4.079 E(IMPR)=6.432 E(VDW )=-1.562 E(ELEC)=-76.778 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 10 steps ----------------------- | E(kin)+E(total)=0.109 E(kin)=3.032 temperature=53.532 | | Etotal =3.120 grad(E)=4.342 E(BOND)=1.036 E(ANGL)=3.220 | | E(DIHE)=0.055 E(IMPR)=2.529 E(VDW )=0.402 E(ELEC)=0.884 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- averages for last 20 steps ----------------------------- | E(kin)+E(total)=8.906 E(kin)=44.748 temperature=790.107 | | Etotal =-35.842 grad(E)=38.975 E(BOND)=12.414 E(ANGL)=17.706 | | E(DIHE)=3.873 E(IMPR)=9.397 E(VDW )=-1.532 E(ELEC)=-77.700 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 20 steps ----------------------- | E(kin)+E(total)=0.172 E(kin)=8.858 temperature=156.413 | | Etotal =9.006 grad(E)=6.928 E(BOND)=5.306 E(ANGL)=4.792 | | E(DIHE)=0.230 E(IMPR)=4.017 E(VDW )=0.501 E(ELEC)=1.143 | | 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 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>close pick1.dat end %X-PLOR>-ERR: File pick1.dat was not open. X-PLOR> X-PLOR> X-PLOR>dynamics analysis DYNAmics-analysis-qualifier= pick bond ( atom tryp 1 ca ) ( atom tryp 1 cb ) geometry PICK> input=pick1.dat begin=2 skip=2 stop=24 OUTPUT=OUTPUT PICK>end REMARKS FILENAME="/home/schwitrs/xplor/test/pick1.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 15:23:30 created by user: schwitrs READC: reading file= 1 ISTART= 2 READC: 19 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 2 SKIP= 2 STOP= 24 READC: TIMEstep= 0.00100000 ps header= CORD 0.002000 1.566995 0.004000 1.602747 0.006000 1.629263 0.008000 1.642237 0.010000 1.639434 0.012000 1.621064 0.014000 1.589867 0.016000 1.551065 0.018000 1.511945 0.020000 1.480640 0.022000 1.464180 READC: complete. 12 coordinate sets were passed to calling routine 0.024000 1.466483 X-PLOR> X-PLOR>pick bond ( atom tryp 1 ca ) ( atom tryp 1 cb ) geometry X-PLOR> X-PLOR> X-PLOR> X-PLOR>dynamics analysis DYNAmics-analysis-qualifier= pick dihedral SELRPN> (atom tryp 1 n) (atom tryp 1 ca) (atom tryp 1 cb) (atom tryp 1 cg) energy PICK> input=pick1.dat begin=2 skip=2 stop=24 OUTPUT=OUTPUT PICK>end REMARKS FILENAME="/home/schwitrs/xplor/test/pick1.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 15:23:30 created by user: schwitrs READC: reading file= 1 ISTART= 2 READC: 19 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 2 SKIP= 2 STOP= 24 READC: TIMEstep= 0.00100000 ps header= CORD 0.002000 0.000668 0.004000 0.004656 0.006000 0.007065 0.008000 0.008016 0.010000 0.009705 0.012000 0.012581 0.014000 0.017011 0.016000 0.026712 0.018000 0.047830 0.020000 0.078205 0.022000 0.097994 READC: complete. 12 coordinate sets were passed to calling routine 0.024000 0.089443 X-PLOR> X-PLOR>pick dihedral SELRPN> (atom tryp 1 n) (atom tryp 1 ca) (atom tryp 1 cb) (atom tryp 1 cg) energy X-PLOR> X-PLOR>dynamics analysis DYNAmics-analysis-qualifier= pick ring SELRPN> (name ca)(name cb)(name cg)(name cd2)(name c) pucker PICK> input=pick1.dat begin=2 skip=2 stop=24 OUTPUT=OUTPUT PICK>end REMARKS FILENAME="/home/schwitrs/xplor/test/pick1.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 15:23:30 created by user: schwitrs READC: reading file= 1 ISTART= 2 READC: 19 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 2 SKIP= 2 STOP= 24 READC: TIMEstep= 0.00100000 ps header= CORD 0.002000 0.711255 13.955580 0.004000 0.725303 14.606426 0.006000 0.729367 15.123412 0.008000 0.720184 15.277294 0.010000 0.697510 14.900363 0.012000 0.664821 13.895915 0.014000 0.628440 12.251300 0.016000 0.595775 10.082898 0.018000 0.573431 7.700541 0.020000 0.565649 5.595337 0.022000 0.573390 4.257366 READC: complete. 12 coordinate sets were passed to calling routine 0.024000 0.594339 3.908404 X-PLOR> X-PLOR>pick ring SELRPN> (name ca)(name cb)(name cg)(name cd2)(name c) pucker PUCKer= 0.594339 3.908404 X-PLOR> X-PLOR>close pick1.dat end X-PLOR>open pick1.dat access=append end close pick1.dat disp=delete end X-PLOR>stop HEAP: maximum use= 631006 current use= 610470 X-PLOR: total CPU time= 0.0500 s X-PLOR: entry time at 15:23:30 11-Jun-07 X-PLOR: exit time at 15:23:30 11-Jun-07