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 15:22:23 X-PLOR>remarks DYNTEST3.INP X-PLOR>remarks test tcoupling dynamics X-PLOR> X-PLOR>topology @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>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=6.2 aon=50.0 HBDSET> aoff=70.0 acut=90.0 HBDSET> end PARRDR> nbonds NBDSET> atom cdie shift eps=1.0 NBDSET> cutnb=100. ctonnb=98.0 ctofnb=99.0 NBDSET> nbxmod=5 vswitch NBDSET> end PARRDR>end X-PLOR> X-PLOR> X-PLOR>vector do ( fbeta=500. ) ( all ) SELRPN: 19 atoms have been selected out of 19 X-PLOR>coor copy end COOR: selected main coordinates copied to comp X-PLOR> X-PLOR> X-PLOR>{* overall t-coupling *} X-PLOR>set seed=311 end X-PLOR>dynamics verlet DYNAmics> nstep=500 timestep=0.001 DYNAmics> NSTEP=500 TIMESTEP=0.001 DYNAmics> iasvel=maxwell firsttemp=300. DYNAmics> tcoupling=true tbath=300. DYNAmics> nprint=100 iprfrq=200 iscvel=0 DYNAmics>end DYNAMC: number of degrees of freedom= 57 ASSVEL: velocities assigned at 300.0000 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] : 1.07213 0.94154 3.47523 ang. mom. [amu A/ps] : 35.25596 -581.46713 -638.61424 kin. ener. [Kcal/mol] : 3.44446 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)=-44.917 E(kin)=16.835 temperature=297.260 | | 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 | ------------------------------------------------------------------------------- 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 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 --------------- step= 100 at 0.10000 ps -------------------------------- | E(kin)+E(total)=-37.735 E(kin)=17.473 temperature=308.518 | | Etotal =-55.208 grad(E)=21.804 E(BOND)=3.146 E(ANGL)=12.553 | | E(DIHE)=4.270 E(IMPR)=5.279 E(VDW )=-1.588 E(ELEC)=-78.867 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- 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 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 --------------- step= 200 at 0.20000 ps -------------------------------- | E(kin)+E(total)=-38.587 E(kin)=18.503 temperature=326.706 | | Etotal =-57.090 grad(E)=22.783 E(BOND)=6.137 E(ANGL)=11.854 | | E(DIHE)=4.327 E(IMPR)=1.824 E(VDW )=-1.829 E(ELEC)=-79.403 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- averages for last 200 steps ----------------------------- | E(kin)+E(total)=-40.193 E(kin)=16.982 temperature=299.852 | | Etotal =-57.175 grad(E)=22.494 E(BOND)=4.988 E(ANGL)=11.451 | | E(DIHE)=2.688 E(IMPR)=4.490 E(VDW )=-0.554 E(ELEC)=-80.238 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 200 steps ----------------------- | E(kin)+E(total)=3.857 E(kin)=0.989 temperature=17.466 | | Etotal =3.737 grad(E)=2.439 E(BOND)=1.697 E(ANGL)=2.194 | | E(DIHE)=1.286 E(IMPR)=1.582 E(VDW )=1.735 E(ELEC)=2.653 | | 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 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 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 --------------- step= 300 at 0.30000 ps -------------------------------- | E(kin)+E(total)=-40.435 E(kin)=15.892 temperature=280.609 | | Etotal =-56.327 grad(E)=18.206 E(BOND)=3.073 E(ANGL)=16.308 | | E(DIHE)=4.289 E(IMPR)=2.715 E(VDW )=0.590 E(ELEC)=-83.303 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- 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 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: 1 distance exclusions and 5 angle exclusions HBONDS: 0 fixed h-bonds, currently 2 h-bonds present --------------- step= 400 at 0.40000 ps -------------------------------- | E(kin)+E(total)=-37.501 E(kin)=15.652 temperature=276.363 | | Etotal =-53.152 grad(E)=24.359 E(BOND)=6.757 E(ANGL)=13.344 | | E(DIHE)=2.931 E(IMPR)=3.286 E(VDW )=0.541 E(ELEC)=-80.012 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- averages for last 200 steps ----------------------------- | E(kin)+E(total)=-40.641 E(kin)=16.969 temperature=299.629 | | Etotal =-57.610 grad(E)=22.902 E(BOND)=5.119 E(ANGL)=12.051 | | E(DIHE)=2.664 E(IMPR)=4.251 E(VDW )=-1.297 E(ELEC)=-80.398 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 200 steps ----------------------- | E(kin)+E(total)=3.891 E(kin)=0.834 temperature=14.731 | | Etotal =3.835 grad(E)=2.651 E(BOND)=1.577 E(ANGL)=1.934 | | E(DIHE)=1.614 E(IMPR)=1.902 E(VDW )=1.109 E(ELEC)=1.580 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- averages for last 400 steps ----------------------------- | E(kin)+E(total)=-40.417 E(kin)=16.976 temperature=299.740 | | Etotal =-57.393 grad(E)=22.698 E(BOND)=5.054 E(ANGL)=11.751 | | E(DIHE)=2.676 E(IMPR)=4.370 E(VDW )=-0.926 E(ELEC)=-80.318 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 400 steps ----------------------- | E(kin)+E(total)=3.881 E(kin)=0.915 temperature=16.157 | | Etotal =3.792 grad(E)=2.555 E(BOND)=1.639 E(ANGL)=2.090 | | E(DIHE)=1.459 E(IMPR)=1.753 E(VDW )=1.503 E(ELEC)=2.185 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- HBONDS: allocating space for 5 h-bond interactions. HBONDS: 1 distance exclusions and 5 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 5 angle exclusions HBONDS: 0 fixed h-bonds, currently 1 h-bonds present --------------- step= 500 at 0.50000 ps -------------------------------- | E(kin)+E(total)=-39.686 E(kin)=16.181 temperature=285.709 | | Etotal =-55.867 grad(E)=22.782 E(BOND)=3.511 E(ANGL)=17.495 | | E(DIHE)=1.002 E(IMPR)=5.886 E(VDW )=-0.140 E(ELEC)=-83.620 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- 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>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 15:22:23 created by user: schwitrs ATOM 1 HT1 TRP 1 1.326 -0.537 -1.149 1.00 0.00 TRYP ATOM 2 HT2 TRP 1 -0.122 -0.090 -0.227 1.00 0.00 TRYP ATOM 3 N TRP 1 0.736 0.193 -0.731 1.00 0.00 TRYP ATOM 4 HT3 TRP 1 0.317 0.789 -1.479 1.00 0.00 TRYP ATOM 5 CA TRP 1 1.352 1.145 0.158 1.00 0.00 TRYP ATOM 6 CB TRP 1 2.587 1.767 -0.417 1.00 0.00 TRYP ATOM 7 CG TRP 1 3.864 0.939 -0.721 1.00 0.00 TRYP ATOM 8 CD2 TRP 1 4.431 0.636 -1.949 1.00 0.00 TRYP ATOM 9 CE2 TRP 1 5.650 0.052 -1.641 1.00 0.00 TRYP ATOM 10 CE3 TRP 1 3.885 0.839 -3.157 1.00 0.00 TRYP ATOM 11 CD1 TRP 1 4.744 0.506 0.264 1.00 0.00 TRYP ATOM 12 NE1 TRP 1 5.833 0.062 -0.349 1.00 0.00 TRYP ATOM 13 HE1 TRP 1 6.499 -0.463 0.135 1.00 0.00 TRYP ATOM 14 CZ2 TRP 1 6.330 -0.501 -2.672 1.00 0.00 TRYP ATOM 15 CZ3 TRP 1 4.501 0.172 -4.185 1.00 0.00 TRYP ATOM 16 CH2 TRP 1 5.701 -0.456 -3.914 1.00 0.00 TRYP ATOM 17 C TRP 1 0.197 2.146 0.271 1.00 0.00 TRYP ATOM 18 OT1 TRP 1 -0.478 2.420 -0.667 1.00 0.00 TRYP ATOM 19 OT2 TRP 1 -0.016 2.573 1.390 1.00 0.00 TRYP END X-PLOR>vector do (store4=mass*$timfac^2*(vx^2+vy^2+vz^2)/(3*$kboltz)) ( all ) SELRPN: 19 atoms have been selected out of 19 X-PLOR>vector show elem ( store4 ) ( all ) SELRPN: 19 atoms have been selected out of 19 ( TRYP TRP 1 HT1 ) 518.27 ( TRYP TRP 1 HT2 ) 96.676 ( TRYP TRP 1 N ) 148.11 ( TRYP TRP 1 HT3 ) 254.81 ( TRYP TRP 1 CA ) 473.66 ( TRYP TRP 1 CB ) 650.00 ( TRYP TRP 1 CG ) 89.920 ( TRYP TRP 1 CD2 ) 468.98 ( TRYP TRP 1 CE2 ) 28.050 ( TRYP TRP 1 CE3 ) 287.08 ( TRYP TRP 1 CD1 ) 17.961 ( TRYP TRP 1 NE1 ) 191.24 ( TRYP TRP 1 HE1 ) 683.45 ( TRYP TRP 1 CZ2 ) 444.40 ( TRYP TRP 1 CZ3 ) 204.72 ( TRYP TRP 1 CH2 ) 261.99 ( TRYP TRP 1 C ) 318.76 ( TRYP TRP 1 OT1 ) 98.749 ( TRYP TRP 1 OT2 ) 191.65 X-PLOR> X-PLOR>stop HEAP: maximum use= 631006 current use= 605745 X-PLOR: total CPU time= 0.0700 s X-PLOR: entry time at 15:22:23 11-Jun-07 X-PLOR: exit time at 15:22:23 11-Jun-07