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 15:21:08 X-PLOR>remarks dsele.inp X-PLOR>remarks test double selection facilities X-PLOR>remarks Thomas Simonson X-PLOR>remarks ================ 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>parameter PARRDR> nbonds NBDSET> atom cdie shift eps=1.0 NBDSET> cutnb=100.0 NBDSET> nbxmod=5 vswitch NBDSET> end PARRDR>end X-PLOR> X-PLOR>segment SEGMENT> name=tryp 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>energy end MAKINB: mode 5 found 83 exclusions, 20 interactions(1-4) and 63 GB exclusions --------------- cycle= 1 -------------------------------------------------- | Etotal =-34.629 grad(E)=13.467 E(BOND)=2.002 E(ANGL)=5.003 | | E(DIHE)=3.599 E(IMPR)=6.918 E(VDW )=-2.124 E(ELEC)=-50.027 | ------------------------------------------------------------------------------- X-PLOR>pick bond (name CA) (name CB) energy SELRPN: 1 atoms have been selected out of 19 SELRPN: 1 atoms have been selected out of 19 ENER= 0.012898 X-PLOR>pick angle (name CA) (name CB) (name CG) energy SELRPN: 1 atoms have been selected out of 19 SELRPN: 1 atoms have been selected out of 19 SELRPN: 1 atoms have been selected out of 19 ENER= 0.002611 X-PLOR>pick angle (name CA) (name CB) (name CG) geometry SELRPN: 1 atoms have been selected out of 19 SELRPN: 1 atoms have been selected out of 19 SELRPN: 1 atoms have been selected out of 19 GEOM= 112.849927 X-PLOR>print threshold=3. 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 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 CD2 |TRYP 1 CE2 |TRYP 1 NE1 ) 112.206 109.000 3.206 0.203 65.000 (TRYP 1 CD2 |TRYP 1 CE3 |TRYP 1 CZ3 ) 115.606 119.000 -3.394 0.316 90.000 Number of violations greater 3.000: 6 RMS deviation= 2.915 X-PLOR> X-PLOR>{* subdivide molecule into two parts *} X-PLOR>{=====================================} X-PLOR> X-PLOR>constraints CONS> interaction (name HT* or name N or name CA or name C or name OT*) SELRPN: 8 atoms have been selected out of 19 SELRPN> (prev) SELRPN: 8 atoms have been selected out of 19 CONS> weights bond 0.10 angle 0.20 dihe 0.30 impr 0.40 vdw 0.50 elec 0.60 end CONS> interaction (name HT* or name N or name CA or name C or name OT*) SELRPN: 8 atoms have been selected out of 19 SELRPN> (prev) SELRPN: 8 atoms have been selected out of 19 CONS> weights bond 0.90 angle 0.80 dihe 0.70 impr 0.60 vdw 0.50 elec 0.40 end CONS> interaction (name HT* or name N or name CA or name C or name OT*) SELRPN: 8 atoms have been selected out of 19 SELRPN> (not (prev)) SELRPN: 11 atoms have been selected out of 19 CONS> interaction (not (name HT* or name N or name CA or name C or name OT*)) SELRPN: 11 atoms have been selected out of 19 SELRPN> (prev) SELRPN: 11 atoms have been selected out of 19 CONS> ? FIX : 0 atoms fixed INTE: 4 active double selections --------------- double selection 1 --------------------------------------- | WEIGhts : | | E(BOND)=0.100 E(ANGL)=0.200 E(DIHE)=0.300 E(IMPR)=0.400 | | E(VDW )=0.500 E(ELEC)=0.600 | ------------------------------------------------------------------------------- --------------- double selection 2 --------------------------------------- | WEIGhts : | | E(BOND)=0.900 E(ANGL)=0.800 E(DIHE)=0.700 E(IMPR)=0.600 | | E(VDW )=0.500 E(ELEC)=0.400 | ------------------------------------------------------------------------------- --------------- double selection 3 --------------------------------------- | WEIGhts : | | E(BOND)=1.000 E(ANGL)=1.000 E(DIHE)=1.000 E(IMPR)=1.000 | | E(VDW )=1.000 E(ELEC)=1.000 | ------------------------------------------------------------------------------- --------------- double selection 4 --------------------------------------- | WEIGhts : | | E(BOND)=1.000 E(ANGL)=1.000 E(DIHE)=1.000 E(IMPR)=1.000 | | E(VDW )=1.000 E(ELEC)=1.000 | ------------------------------------------------------------------------------- CONS>end X-PLOR> X-PLOR>energy end MAKINB: mode 5 found 22 exclusions, 5 interactions(1-4) and 17 GB exclusions MAKINB: mode 5 found 22 exclusions, 5 interactions(1-4) and 17 GB exclusions MAKINB: mode 5 found 13 exclusions, 9 interactions(1-4) and 4 GB exclusions MAKINB: mode 5 found 48 exclusions, 6 interactions(1-4) and 42 GB exclusions --------------- cycle= 2 -------------------------------------------------- | Etotal =-34.629 grad(E)=13.467 E(BOND)=2.002 E(ANGL)=5.003 | | E(DIHE)=3.599 E(IMPR)=6.918 E(VDW )=-2.124 E(ELEC)=-50.027 | ------------------------------------------------------------------------------- X-PLOR>pick bond (name CA) (name CB) energy SELRPN: 1 atoms have been selected out of 19 SELRPN: 1 atoms have been selected out of 19 ENER= 0.012898 X-PLOR>pick angle (name CA) (name CB) (name CG) energy SELRPN: 1 atoms have been selected out of 19 SELRPN: 1 atoms have been selected out of 19 SELRPN: 1 atoms have been selected out of 19 ENER= 0.002611 X-PLOR>pick angle (name CA) (name CB) (name CG) geometry SELRPN: 1 atoms have been selected out of 19 SELRPN: 1 atoms have been selected out of 19 SELRPN: 1 atoms have been selected out of 19 GEOM= 112.849927 X-PLOR>print threshold=3. 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 (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 (atom-i |atom-j |atom-k ) angle equil. delta energy const. (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 (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 CD2 |TRYP 1 CE2 |TRYP 1 NE1 ) 112.206 109.000 3.206 0.203 65.000 (TRYP 1 CD2 |TRYP 1 CE3 |TRYP 1 CZ3 ) 115.606 119.000 -3.394 0.316 90.000 Number of violations greater 3.000: 7 RMS deviation= 2.656 X-PLOR>vector show element (DX) (all) SELRPN: 19 atoms have been selected out of 19 ( TRYP TRP 1 HT1 ) 2.1272 ( TRYP TRP 1 HT2 ) 4.9782 ( TRYP TRP 1 N ) -19.200 ( TRYP TRP 1 HT3 ) 2.4906 ( TRYP TRP 1 CA ) 25.456 ( TRYP TRP 1 CB ) -3.0373 ( TRYP TRP 1 CG ) -28.501 ( TRYP TRP 1 CD2 ) 52.977 ( TRYP TRP 1 CE2 ) -33.664 ( TRYP TRP 1 CE3 ) -29.554 ( TRYP TRP 1 CD1 ) 6.5187 ( TRYP TRP 1 NE1 ) 31.078 ( TRYP TRP 1 HE1 ) -16.383 ( TRYP TRP 1 CZ2 ) 19.585 ( TRYP TRP 1 CZ3 ) 3.5754 ( TRYP TRP 1 CH2 ) -3.7797 ( TRYP TRP 1 C ) 4.1335 ( TRYP TRP 1 OT1 ) -9.8901 ( TRYP TRP 1 OT2 ) -8.9115 X-PLOR>vector show element (DY) (all) SELRPN: 19 atoms have been selected out of 19 ( TRYP TRP 1 HT1 ) -4.1180 ( TRYP TRP 1 HT2 ) -1.3887 ( TRYP TRP 1 N ) -20.158 ( TRYP TRP 1 HT3 ) -5.3588 ( TRYP TRP 1 CA ) 8.8018 ( TRYP TRP 1 CB ) 4.6827 ( TRYP TRP 1 CG ) 18.354 ( TRYP TRP 1 CD2 ) -39.563 ( TRYP TRP 1 CE2 ) 14.832 ( TRYP TRP 1 CE3 ) 19.605 ( TRYP TRP 1 CD1 ) -18.440 ( TRYP TRP 1 NE1 ) 19.142 ( TRYP TRP 1 HE1 ) -9.6683 ( TRYP TRP 1 CZ2 ) -9.7337 ( TRYP TRP 1 CZ3 ) -1.5489 ( TRYP TRP 1 CH2 ) 2.9424 ( TRYP TRP 1 C ) 28.334 ( TRYP TRP 1 OT1 ) -1.9048 ( TRYP TRP 1 OT2 ) -4.8120 X-PLOR>vector show element (DZ) (all) SELRPN: 19 atoms have been selected out of 19 ( TRYP TRP 1 HT1 ) -3.5901 ( TRYP TRP 1 HT2 ) -5.0898 ( TRYP TRP 1 N ) -27.816 ( TRYP TRP 1 HT3 ) -1.0908 ( TRYP TRP 1 CA ) 35.396 ( TRYP TRP 1 CB ) 4.9996 ( TRYP TRP 1 CG ) -13.236 ( TRYP TRP 1 CD2 ) -2.6422 ( TRYP TRP 1 CE2 ) 24.926 ( TRYP TRP 1 CE3 ) 6.9457 ( TRYP TRP 1 CD1 ) -1.7337 ( TRYP TRP 1 NE1 ) -38.506 ( TRYP TRP 1 HE1 ) -0.87584 ( TRYP TRP 1 CZ2 ) 16.209 ( TRYP TRP 1 CZ3 ) 3.7135 ( TRYP TRP 1 CH2 ) 1.8511 ( TRYP TRP 1 C ) -6.4323 ( TRYP TRP 1 OT1 ) 15.989 ( TRYP TRP 1 OT2 ) -9.0157 X-PLOR> X-PLOR> X-PLOR>{* Create a perturbation by placing an additional charge on HT1 *} X-PLOR>{================================================================} X-PLOR> X-PLOR>constraints CONS> interaction (name HT1) (not name HT1) SELRPN: 1 atoms have been selected out of 19 SELRPN: 18 atoms have been selected out of 19 CONS> vweight * 0. elec 1. end CONS> interaction (not name HT1) (not name HT1) {zero vweight by default} SELRPN: 18 atoms have been selected out of 19 SELRPN: 18 atoms have been selected out of 19 CONS>end X-PLOR> X-PLOR>{* exp(-V/kT) averaging *} X-PLOR>set seed=271828. end X-PLOR>dynamics verlet DYNAmics> iasvel=maxwell firsttemp=298. DYNAmics> iasors=1 finaltemp=298. DYNAmics> nstep=10 timestep=0.001 DYNAmics> iprfrq=5 DYNAmics> tcoupling=true tbath=298. DYNAmics> trajectory=coor.dat nsavc=1 DYNAmics> velocity=vel.dat nsavv=1 DYNAmics>end ASSFIL: file /home/schwitrs/xplor/test/coor.dat opened. ASSFIL: file /home/schwitrs/xplor/test/vel.dat opened. DYNAMC: number of degrees of freedom= 57 ASSVEL: velocities assigned at 298.0000 K, SEED= 271828.000 ASSVEL: maxwell distribution CENMAS: Information about center of free masses position [A] : 3.15083 0.85925 -1.15799 velocity [A/ps] : 1.36997 -0.97150 0.89849 ang. mom. [amu A/ps] : -19.98063 -425.45856 -291.98269 kin. ener. [Kcal/mol] : 0.88543 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 6 exclusions, 2 interactions(1-4) and 4 GB exclusions MAKINB: mode 5 found 77 exclusions, 18 interactions(1-4) and 59 GB exclusions --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=-18.648 E(kin)=15.981 temperature=282.173 | | Etotal =-34.629 grad(E)=13.467 E(BOND)=2.002 E(ANGL)=5.003 | | E(DIHE)=3.599 E(IMPR)=6.918 E(VDW )=-2.124 E(ELEC)=-50.027 | | Vpert =-25.261 | ------------------------------------------------------------------------------- WRITEC: CORD sets starting from step 1 are written every 1 steps WRITEC: where 19 atoms are "free" --------------- step= 1 at 0.00100 ps -------------------------------- | E(kin)+E(total)=-18.625 E(kin)=15.137 temperature=267.270 | | Etotal =-33.762 grad(E)=14.111 E(BOND)=2.081 E(ANGL)=5.133 | | E(DIHE)=3.602 E(IMPR)=7.551 E(VDW )=-2.086 E(ELEC)=-50.042 | | Vpert =-25.142 | ------------------------------------------------------------------------------- WRITEC: VELD sets starting from step 1 are written every 1 steps WRITEC: where 19 atoms are "free" --------------- step= 2 at 0.00200 ps -------------------------------- | E(kin)+E(total)=-18.560 E(kin)=13.281 temperature=234.499 | | Etotal =-31.840 grad(E)=17.152 E(BOND)=3.176 E(ANGL)=5.551 | | E(DIHE)=3.602 E(IMPR)=7.994 E(VDW )=-2.018 E(ELEC)=-50.145 | | Vpert =-25.101 | ------------------------------------------------------------------------------- --------------- step= 3 at 0.00300 ps -------------------------------- | E(kin)+E(total)=-18.509 E(kin)=11.325 temperature=199.969 | | Etotal =-29.834 grad(E)=20.614 E(BOND)=4.422 E(ANGL)=6.165 | | E(DIHE)=3.601 E(IMPR)=8.199 E(VDW )=-1.916 E(ELEC)=-50.305 | | Vpert =-25.145 | ------------------------------------------------------------------------------- --------------- step= 4 at 0.00400 ps -------------------------------- | E(kin)+E(total)=-18.500 E(kin)=10.023 temperature=176.981 | | Etotal =-28.524 grad(E)=23.423 E(BOND)=5.187 E(ANGL)=6.841 | | E(DIHE)=3.600 E(IMPR)=8.136 E(VDW )=-1.782 E(ELEC)=-50.506 | | Vpert =-25.270 | ------------------------------------------------------------------------------- --------------- step= 5 at 0.00500 ps -------------------------------- | E(kin)+E(total)=-18.511 E(kin)=9.565 temperature=168.881 | | Etotal =-28.076 grad(E)=25.285 E(BOND)=5.471 E(ANGL)=7.438 | | E(DIHE)=3.598 E(IMPR)=7.796 E(VDW )=-1.625 E(ELEC)=-50.754 | | Vpert =-25.467 | ------------------------------------------------------------------------------- --------------- averages for last 5 steps ----------------------------- | E(kin)+E(total)=-18.541 E(kin)=11.866 temperature=209.520 | | Etotal =-30.407 grad(E)=20.117 E(BOND)=4.067 E(ANGL)=6.226 | | E(DIHE)=3.601 E(IMPR)=7.935 E(VDW )=-1.885 E(ELEC)=-50.350 | | Vpert =-25.225 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 5 steps ----------------------- | E(kin)+E(total)=0.047 E(kin)=2.083 temperature=36.771 | | Etotal =2.127 grad(E)=4.068 E(BOND)=1.272 E(ANGL)=0.837 | | E(DIHE)=0.002 E(IMPR)=0.237 E(VDW )=0.166 E(ELEC)=0.256 | | Vpert =0.134 | ------------------------------------------------------------------------------- --------------- step= 6 at 0.00600 ps -------------------------------- | E(kin)+E(total)=-18.507 E(kin)=9.863 temperature=174.150 | | Etotal =-28.370 grad(E)=26.039 E(BOND)=5.513 E(ANGL)=7.852 | | E(DIHE)=3.597 E(IMPR)=7.203 E(VDW )=-1.458 E(ELEC)=-51.076 | | Vpert =-25.721 | ------------------------------------------------------------------------------- --------------- step= 7 at 0.00700 ps -------------------------------- | E(kin)+E(total)=-18.494 E(kin)=10.992 temperature=194.077 | | Etotal =-29.486 grad(E)=25.342 E(BOND)=5.263 E(ANGL)=8.046 | | E(DIHE)=3.596 E(IMPR)=6.407 E(VDW )=-1.296 E(ELEC)=-51.503 | | Vpert =-26.016 | ------------------------------------------------------------------------------- --------------- step= 8 at 0.00800 ps -------------------------------- | E(kin)+E(total)=-18.510 E(kin)=13.098 temperature=231.273 | | Etotal =-31.609 grad(E)=22.841 E(BOND)=4.440 E(ANGL)=8.066 | | E(DIHE)=3.594 E(IMPR)=5.491 E(VDW )=-1.144 E(ELEC)=-52.055 | | Vpert =-26.336 | ------------------------------------------------------------------------------- --------------- step= 9 at 0.00900 ps -------------------------------- | E(kin)+E(total)=-18.572 E(kin)=15.900 temperature=280.745 | | Etotal =-34.472 grad(E)=18.648 E(BOND)=3.103 E(ANGL)=8.022 | | E(DIHE)=3.591 E(IMPR)=4.549 E(VDW )=-1.003 E(ELEC)=-52.733 | | Vpert =-26.671 | ------------------------------------------------------------------------------- --------------- step= 10 at 0.01000 ps -------------------------------- | E(kin)+E(total)=-18.641 E(kin)=18.491 temperature=326.488 | | Etotal =-37.131 grad(E)=13.928 E(BOND)=1.918 E(ANGL)=8.058 | | E(DIHE)=3.586 E(IMPR)=3.672 E(VDW )=-0.857 E(ELEC)=-53.508 | | Vpert =-27.011 | ------------------------------------------------------------------------------- --------------- averages for last 5 steps ----------------------------- | E(kin)+E(total)=-18.545 E(kin)=13.669 temperature=241.347 | | Etotal =-32.213 grad(E)=21.360 E(BOND)=4.048 E(ANGL)=8.009 | | E(DIHE)=3.593 E(IMPR)=5.464 E(VDW )=-1.152 E(ELEC)=-52.175 | | Vpert =-26.351 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 5 steps ----------------------- | E(kin)+E(total)=0.055 E(kin)=3.169 temperature=55.951 | | Etotal =3.221 grad(E)=4.529 E(BOND)=1.357 E(ANGL)=0.080 | | E(DIHE)=0.004 E(IMPR)=1.262 E(VDW )=0.212 E(ELEC)=0.867 | | Vpert =0.458 | ------------------------------------------------------------------------------- --------------- averages for last 10 steps ----------------------------- | E(kin)+E(total)=-18.543 E(kin)=12.767 temperature=225.433 | | Etotal =-31.310 grad(E)=20.738 E(BOND)=4.057 E(ANGL)=7.117 | | E(DIHE)=3.597 E(IMPR)=6.700 E(VDW )=-1.518 E(ELEC)=-51.263 | | Vpert =-25.788 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 10 steps ----------------------- | E(kin)+E(total)=0.051 E(kin)=2.829 temperature=49.945 | | Etotal =2.875 grad(E)=4.349 E(BOND)=1.315 E(ANGL)=1.072 | | E(DIHE)=0.005 E(IMPR)=1.533 E(VDW )=0.413 E(ELEC)=1.114 | | Vpert =0.656 | ------------------------------------------------------------------------------- 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>display $AVE_PERT $AVE_ELEC -25.788 -51.2628 X-PLOR> X-PLOR> X-PLOR>{now calculate the free energy change "by hand" through the command language} X-PLOR>constraints interaction (name HT1) (not name HT1) end SELRPN: 1 atoms have been selected out of 19 SELRPN: 18 atoms have been selected out of 19 X-PLOR>energy accum=reset end X-PLOR>flags FLAGS> exclude * FLAGS> include elec FLAGS>end X-PLOR> X-PLOR>{initializations for post-averaging of exp(-V/kT)} X-PLOR>read trajectory begin=1 skip=1 stop=10 READ-TRAJectory> input=coor.dat ASSFIL: file /home/schwitrs/xplor/test/coor.dat opened. READ-TRAJectory>end REMARKS FILENAME="/home/schwitrs/xplor/test/coor.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 15:21:09 created by user: schwitrs READC: reading file= 1 ISTART= 1 READC: 19 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 1 SKIP= 1 STOP= 10 READC: TIMEstep= 0.00100000 ps header= CORD READ-TRAJectory: frame # 1 has been copied to the main coordinate set. X-PLOR>energy end MAKINB: mode 5 found 6 exclusions, 2 interactions(1-4) and 4 GB exclusions --------------- cycle= 1 -------------------------------------------------- | Etotal =-25.142 grad(E)=2.718 E(ELEC)=-25.142 | | Vpert =0.000 | ------------------------------------------------------------------------------- X-PLOR>evaluate ( $N=1) EVALUATE: symbol $N set to 1.00000 (real) X-PLOR>evaluate ( $V =-$ELEC/(298.*$KBOLTZ) ) EVALUATE: symbol $V set to 42.4562 (real) X-PLOR>evaluate ( $E = exp($V) ) EVALUATE: symbol $E set to 0.274471E+19 (real) X-PLOR> X-PLOR>{loop for post-averaging} X-PLOR> X-PLOR>while ($N < 10) loop main NEXTCD: condition evaluated as true X-PLOR>read trajectory next end READCP: trajectory number 2 has been copied to the main coordinate set X-PLOR>energy end --------------- cycle= 2 -------------------------------------------------- | Etotal =-25.101 grad(E)=2.711 E(ELEC)=-25.101 | | Vpert =0.000 | ------------------------------------------------------------------------------- X-PLOR>evaluate ( $V =-$ELEC/(298.*$KBOLTZ) ) EVALUATE: symbol $V set to 42.3872 (real) X-PLOR>evaluate ( $E = $E + exp($V) ) EVALUATE: symbol $E set to 0.530647E+19 (real) X-PLOR>evaluate ( $N = $N+1.) EVALUATE: symbol $N set to 2.00000 (real) X-PLOR>end loop main X-PLOR>while ($N < 10) loop main NEXTCD: condition evaluated as true X-PLOR>read trajectory next end READCP: trajectory number 3 has been copied to the main coordinate set X-PLOR>energy end --------------- cycle= 3 -------------------------------------------------- | Etotal =-25.145 grad(E)=2.714 E(ELEC)=-25.145 | | Vpert =0.000 | ------------------------------------------------------------------------------- X-PLOR>evaluate ( $V =-$ELEC/(298.*$KBOLTZ) ) EVALUATE: symbol $V set to 42.4608 (real) X-PLOR>evaluate ( $E = $E + exp($V) ) EVALUATE: symbol $E set to 0.806395E+19 (real) X-PLOR>evaluate ( $N = $N+1.) EVALUATE: symbol $N set to 3.00000 (real) X-PLOR>end loop main X-PLOR>while ($N < 10) loop main NEXTCD: condition evaluated as true X-PLOR>read trajectory next end READCP: trajectory number 4 has been copied to the main coordinate set X-PLOR>energy end --------------- cycle= 4 -------------------------------------------------- | Etotal =-25.270 grad(E)=2.728 E(ELEC)=-25.270 | | Vpert =0.000 | ------------------------------------------------------------------------------- X-PLOR>evaluate ( $V =-$ELEC/(298.*$KBOLTZ) ) EVALUATE: symbol $V set to 42.6726 (real) X-PLOR>evaluate ( $E = $E + exp($V) ) EVALUATE: symbol $E set to 0.114718E+20 (real) X-PLOR>evaluate ( $N = $N+1.) EVALUATE: symbol $N set to 4.00000 (real) X-PLOR>end loop main X-PLOR>while ($N < 10) loop main NEXTCD: condition evaluated as true X-PLOR>read trajectory next end READCP: trajectory number 5 has been copied to the main coordinate set X-PLOR>energy end --------------- cycle= 5 -------------------------------------------------- | Etotal =-25.467 grad(E)=2.752 E(ELEC)=-25.467 | | Vpert =0.000 | ------------------------------------------------------------------------------- X-PLOR>evaluate ( $V =-$ELEC/(298.*$KBOLTZ) ) EVALUATE: symbol $V set to 43.0054 (real) X-PLOR>evaluate ( $E = $E + exp($V) ) EVALUATE: symbol $E set to 0.162253E+20 (real) X-PLOR>evaluate ( $N = $N+1.) EVALUATE: symbol $N set to 5.00000 (real) X-PLOR>end loop main X-PLOR>while ($N < 10) loop main NEXTCD: condition evaluated as true X-PLOR>read trajectory next end READCP: trajectory number 6 has been copied to the main coordinate set X-PLOR>energy end --------------- cycle= 6 -------------------------------------------------- | Etotal =-25.721 grad(E)=2.783 E(ELEC)=-25.721 | | Vpert =0.000 | ------------------------------------------------------------------------------- X-PLOR>evaluate ( $V =-$ELEC/(298.*$KBOLTZ) ) EVALUATE: symbol $V set to 43.4344 (real) X-PLOR>evaluate ( $E = $E + exp($V) ) EVALUATE: symbol $E set to 0.235255E+20 (real) X-PLOR>evaluate ( $N = $N+1.) EVALUATE: symbol $N set to 6.00000 (real) X-PLOR>end loop main X-PLOR>while ($N < 10) loop main NEXTCD: condition evaluated as true X-PLOR>read trajectory next end READCP: trajectory number 7 has been copied to the main coordinate set X-PLOR>energy end --------------- cycle= 7 -------------------------------------------------- | Etotal =-26.016 grad(E)=2.820 E(ELEC)=-26.016 | | Vpert =0.000 | ------------------------------------------------------------------------------- X-PLOR>evaluate ( $V =-$ELEC/(298.*$KBOLTZ) ) EVALUATE: symbol $V set to 43.9322 (real) X-PLOR>evaluate ( $E = $E + exp($V) ) EVALUATE: symbol $E set to 0.355351E+20 (real) X-PLOR>evaluate ( $N = $N+1.) EVALUATE: symbol $N set to 7.00000 (real) X-PLOR>end loop main X-PLOR>while ($N < 10) loop main 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>energy end --------------- cycle= 8 -------------------------------------------------- | Etotal =-26.336 grad(E)=2.860 E(ELEC)=-26.336 | | Vpert =0.000 | ------------------------------------------------------------------------------- X-PLOR>evaluate ( $V =-$ELEC/(298.*$KBOLTZ) ) EVALUATE: symbol $V set to 44.4733 (real) X-PLOR>evaluate ( $E = $E + exp($V) ) EVALUATE: symbol $E set to 0.561664E+20 (real) X-PLOR>evaluate ( $N = $N+1.) EVALUATE: symbol $N set to 8.00000 (real) X-PLOR>end loop main X-PLOR>while ($N < 10) loop main NEXTCD: condition evaluated as true X-PLOR>read trajectory next end READCP: trajectory number 9 has been copied to the main coordinate set X-PLOR>energy end --------------- cycle= 9 -------------------------------------------------- | Etotal =-26.671 grad(E)=2.902 E(ELEC)=-26.671 | | Vpert =0.000 | ------------------------------------------------------------------------------- X-PLOR>evaluate ( $V =-$ELEC/(298.*$KBOLTZ) ) EVALUATE: symbol $V set to 45.0377 (real) X-PLOR>evaluate ( $E = $E + exp($V) ) EVALUATE: symbol $E set to 0.924414E+20 (real) X-PLOR>evaluate ( $N = $N+1.) EVALUATE: symbol $N set to 9.00000 (real) X-PLOR>end loop main X-PLOR>while ($N < 10) loop main NEXTCD: condition evaluated as true X-PLOR>read trajectory next end READC: complete. 10 coordinate sets were passed to calling routine READCP: trajectory number 10 has been copied to the main coordinate set X-PLOR>energy end --------------- cycle= 10 -------------------------------------------------- | Etotal =-27.011 grad(E)=2.946 E(ELEC)=-27.011 | | Vpert =0.000 | ------------------------------------------------------------------------------- X-PLOR>evaluate ( $V =-$ELEC/(298.*$KBOLTZ) ) EVALUATE: symbol $V set to 45.6130 (real) X-PLOR>evaluate ( $E = $E + exp($V) ) EVALUATE: symbol $E set to 0.156930E+21 (real) X-PLOR>evaluate ( $N = $N+1.) EVALUATE: symbol $N set to 10.0000 (real) X-PLOR>end loop main X-PLOR>while ($N < 10) loop main NEXTCD: condition evaluated as false X-PLOR>read trajectory next end X-PLOR>energy end X-PLOR>evaluate ( $V =-$ELEC/(298.*$KBOLTZ) ) X-PLOR>evaluate ( $E = $E + exp($V) ) X-PLOR>evaluate ( $N = $N+1.) X-PLOR>end loop main X-PLOR>evaluate ( $E = $E/$N) EVALUATE: symbol $E set to 0.156930E+20 (real) X-PLOR>evaluate ( $A = LOG($E)) EVALUATE: symbol $A set to 44.1997 (real) X-PLOR>evaluate ( $A =-298.*$KBOLTZ*$A) EVALUATE: symbol $A set to -26.1743 (real) X-PLOR>display $A { free energy change } -26.1743 { free energy change } X-PLOR> X-PLOR> X-PLOR>{* now test the hydrogen bonds term *} X-PLOR>structure reset end SCRATC-warning: CONStraints INTEraction selections erased. XPLOR: current counts (number in parenthesis is maximum) NATOM= 0(MAXA= 200) NBOND= 0(MAXB= 100) NTHETA= 0(MAXT= 100) NGRP= 0(MAXGRP= 100) NPHI= 0(MAXP= 100) NIMPHI= 0(MAXIMP= 100) NDON= 0(MAXPAD= 100) NACC= 0(MAXPAD= 100) NNB= 0(MAXNB= 100) X-PLOR> X-PLOR> X-PLOR>segment SEGMENT> name=BET1 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> PRO VAL ASN THR PHE VAL HIS MAPIC: Atom numbers being modified SEQUence-element (terminate with END) = end MAPIC: Atom numbers being modified CHAIN> end SEGMENT>end SEGMNT: 7 residues were inserted into segment "BET1" XPLOR: current counts (number in parenthesis is maximum) NATOM= 71(MAXA= 200) NBOND= 73(MAXB= 100) NTHETA= 107(MAXT= 200) NGRP= 28(MAXGRP= 100) NPHI= 36(MAXP= 100) NIMPHI= 40(MAXIMP= 100) NDON= 13(MAXPAD= 100) NACC= 10(MAXPAD= 100) NNB= 3(MAXNB= 100) X-PLOR> X-PLOR>segment SEGMENT> name=BET2 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> SER ILE THR ASP CYS ARG GLU MAPIC: Atom numbers being modified SEQUence-element (terminate with END) = end MAPIC: Atom numbers being modified CHAIN> end SEGMENT>end SEGMNT: 7 residues were inserted into segment "BET2" XPLOR: current counts (number in parenthesis is maximum) NATOM= 143(MAXA= 200) NBOND= 144(MAXB= 200) NTHETA= 208(MAXT= 400) NGRP= 55(MAXGRP= 100) NPHI= 79(MAXP= 100) NIMPHI= 66(MAXIMP= 100) NDON= 29(MAXPAD= 100) NACC= 24(MAXPAD= 100) NNB= 3(MAXNB= 100) X-PLOR> X-PLOR>coor COOR> remarks coordinates obtained from Greg Petsko COOR> remarks neutron diffraction structure of ribonuclease COOR> natoms=143 COOR> 1 1 PRO HT1 27.19210 7.94321 7.45578 BET1 1 0.00000 X-PLOR>! X-PLOR>! X-PLOR>! TEST HBONDS X-PLOR>! X-PLOR>parameter PARRDR> hbonds HBDSET> acceptor=true don=3.5 doff=4.0 dcut=5.0 aon=50.0 aoff=70. HBDSET> acut=90.0 HBDSET> end PARRDR>end X-PLOR>print hbonds HBONDS: allocating space for 145 h-bond interactions. HBONDS: 588 distance exclusions and 66 angle exclusions HBONDS: 0 fixed h-bonds, currently 39 h-bonds present HBPRIN: list of 39 h-bond pairs HBOND ENERGY DISTANCE 180- A-H-D H-A-AA 1(BET1 1 N -HT1 )(O -C 2 BET1) 0.000 4.597 39.964 87.094 2(BET1 1 N -HT2 )(OE2 -CD 7 BET2) 0.000 4.616 73.002 90.350 3(BET1 2 N -H )(O -C 2 BET1) 0.000 2.748 76.732 95.878 4(BET1 3 N -H )(O -C 1 BET1) 0.000 4.774 85.098 98.334 5(BET1 3 N -H )(O -C 3 BET1) 0.000 2.846 76.787 98.950 6(BET1 3 N -H )(O -C 5 BET2) -1.740 2.990 25.593 29.403 7(BET1 3 ND2 -HD21)(O -C 3 BET1) 0.000 4.290 86.992 111.076 8(BET1 3 ND2 -HD22)(O -C 4 BET1) 0.000 3.852 83.777 69.722 9(BET1 4 N -H )(OD1 -CG 3 BET1) 0.000 3.400 63.051 92.471 10(BET1 4 OG1 -HG1 )(O -C 3 BET1) 0.000 3.800 63.438 108.106 11(BET1 4 OG1 -HG1 )(O -C 3 BET2) 0.000 4.462 78.291 67.190 12(BET1 4 OG1 -HG1 )(OD1 -CG 4 BET2) 0.000 3.530 57.674 88.997 13(BET1 4 OG1 -HG1 )(OD2 -CG 4 BET2) 0.000 4.411 21.493 114.693 14(BET1 5 N -H )(O -C 3 BET1) 0.000 4.383 85.102 89.377 15(BET1 5 N -H )(OG1 - 4 BET1) 0.000 4.474 88.565 0.000 16(BET1 5 N -H )(O -C 3 BET2) -2.148 2.901 18.097 29.883 17(BET1 6 N -H )(O -C 4 BET1) 0.000 4.328 88.058 88.217 18(BET1 7 N -H )(O -C 5 BET1) 0.000 4.289 78.980 89.949 19(BET1 7 N -H )(OG - 1 BET2) 0.000 4.988 48.290 0.000 20(BET1 7 N -H )(O -C 1 BET2) -2.577 2.993 7.746 28.510 21(BET1 7 ND1 -HD1 )(OT2 -C 7 BET1) 0.000 4.903 79.677 99.948 22(BET1 7 NE2 -HE2 )(O -C 2 BET2) 0.000 4.746 69.301 114.156 23(BET1 7 NE2 -HE2 )(OG1 - 3 BET2) -2.087 2.533 11.847 0.000 24(BET2 1 N -HT2 )(OT1 -C 7 BET1) 0.000 4.912 20.225 66.326 25(BET2 1 N -HT2 )(O -C 1 BET2) 0.000 2.789 84.455 98.451 26(BET2 2 N -H )(O -C 2 BET2) 0.000 2.701 80.995 98.364 27(BET2 3 N -H )(O -C 5 BET1) -1.593 2.951 26.447 32.541 28(BET2 3 N -H )(O -C 3 BET2) 0.000 2.853 78.524 104.178 29(BET2 3 OG1 -HG1 )(O -C 2 BET2) 0.000 3.709 72.690 92.317 30(BET2 4 N -H )(O -C 2 BET2) 0.000 4.403 82.432 95.411 31(BET2 5 N -H )(O -C 3 BET1) -1.785 2.862 27.000 25.785 32(BET2 5 N -H )(O -C 3 BET2) 0.000 4.010 86.943 84.198 33(BET2 5 N -H )(OD1 -CG 4 BET2) 0.000 4.866 79.356 139.400 34(BET2 5 N -H )(OD2 -CG 4 BET2) 0.000 3.663 86.979 88.550 35(BET2 5 N -H )(O -C 5 BET2) 0.000 2.832 88.950 101.581 36(BET2 6 N -H )(O -C 4 BET2) 0.000 4.255 78.461 93.004 37(BET2 6 N -H )(O -C 6 BET2) 0.000 2.884 87.525 102.459 38(BET2 7 N -H )(O -C 1 BET1) -2.385 2.947 18.378 23.362 39(BET2 7 N -H )(O -C 5 BET2) 0.000 4.497 82.576 93.889 X-PLOR>flags exclude * include hbonds end X-PLOR>energy end --------------- cycle= 11 -------------------------------------------------- | Etotal =-14.315 grad(E)=1.039 E(HBON)=-14.315 | | Vpert =0.000 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>cons CONS> interaction=( resid 1:2 ) ( prev) SELRPN: 36 atoms have been selected out of 143 SELRPN: 36 atoms have been selected out of 143 CONS> interaction=( resid 1:2 ) ( not prev) SELRPN: 36 atoms have been selected out of 143 SELRPN: 107 atoms have been selected out of 143 CONS> weights hbonds 0.5 end CONS> interaction=( resid 1:2 ) ( not prev) SELRPN: 36 atoms have been selected out of 143 SELRPN: 107 atoms have been selected out of 143 CONS> weights hbonds 0.5 end CONS> interaction=( not resid 1:2) (prev) SELRPN: 107 atoms have been selected out of 143 SELRPN: 107 atoms have been selected out of 143 CONS>end X-PLOR> X-PLOR>print hbonds end HBONDS: allocating space for 53 h-bond interactions. HBONDS: 22 distance exclusions and 13 angle exclusions HBONDS: 654 fixed h-bonds, currently 4 h-bonds present HBPRIN: list of 4 h-bond pairs HBOND ENERGY DISTANCE 180- A-H-D H-A-AA 1(BET1 1 N -HT1 )(O -C 2 BET1) 0.000 4.597 39.964 87.094 2(BET1 2 N -H )(O -C 2 BET1) 0.000 2.748 76.732 95.878 3(BET2 1 N -HT2 )(O -C 1 BET2) 0.000 2.789 84.455 98.451 4(BET2 2 N -H )(O -C 2 BET2) 0.000 2.701 80.995 98.364 HBONDS: allocating space for 145 h-bond interactions. HBONDS: 235 distance exclusions and 13 angle exclusions HBONDS: 436 fixed h-bonds, currently 9 h-bonds present HBPRIN: list of 9 h-bond pairs HBOND ENERGY DISTANCE 180- A-H-D H-A-AA 1(BET1 1 N -HT2 )(OE2 -CD 7 BET2) 0.000 4.616 73.002 90.350 2(BET1 3 N -H )(O -C 1 BET1) 0.000 4.774 85.098 98.334 3(BET1 7 N -H )(OG - 1 BET2) 0.000 4.988 48.290 0.000 4(BET1 7 N -H )(O -C 1 BET2) -2.577 2.993 7.746 28.510 5(BET1 7 NE2 -HE2 )(O -C 2 BET2) 0.000 4.746 69.301 114.156 6(BET2 1 N -HT2 )(OT1 -C 7 BET1) 0.000 4.912 20.225 66.326 7(BET2 3 OG1 -HG1 )(O -C 2 BET2) 0.000 3.709 72.690 92.317 8(BET2 4 N -H )(O -C 2 BET2) 0.000 4.403 82.432 95.411 9(BET2 7 N -H )(O -C 1 BET1) -2.385 2.947 18.378 23.362 HBONDS: allocating space for 145 h-bond interactions. HBONDS: 235 distance exclusions and 13 angle exclusions HBONDS: 436 fixed h-bonds, currently 9 h-bonds present HBPRIN: list of 9 h-bond pairs HBOND ENERGY DISTANCE 180- A-H-D H-A-AA 1(BET1 1 N -HT2 )(OE2 -CD 7 BET2) 0.000 4.616 73.002 90.350 2(BET1 3 N -H )(O -C 1 BET1) 0.000 4.774 85.098 98.334 3(BET1 7 N -H )(OG - 1 BET2) 0.000 4.988 48.290 0.000 4(BET1 7 N -H )(O -C 1 BET2) -2.577 2.993 7.746 28.510 5(BET1 7 NE2 -HE2 )(O -C 2 BET2) 0.000 4.746 69.301 114.156 6(BET2 1 N -HT2 )(OT1 -C 7 BET1) 0.000 4.912 20.225 66.326 7(BET2 3 OG1 -HG1 )(O -C 2 BET2) 0.000 3.709 72.690 92.317 8(BET2 4 N -H )(O -C 2 BET2) 0.000 4.403 82.432 95.411 9(BET2 7 N -H )(O -C 1 BET1) -2.385 2.947 18.378 23.362 HBONDS: allocating space for 145 h-bond interactions. HBONDS: 331 distance exclusions and 40 angle exclusions HBONDS: 296 fixed h-bonds, currently 26 h-bonds present HBPRIN: list of 26 h-bond pairs HBOND ENERGY DISTANCE 180- A-H-D H-A-AA 1(BET1 3 N -H )(O -C 3 BET1) 0.000 2.846 76.787 98.950 2(BET1 3 N -H )(O -C 5 BET2) -1.740 2.990 25.593 29.403 3(BET1 3 ND2 -HD21)(O -C 3 BET1) 0.000 4.290 86.992 111.076 4(BET1 3 ND2 -HD22)(O -C 4 BET1) 0.000 3.852 83.777 69.722 5(BET1 4 N -H )(OD1 -CG 3 BET1) 0.000 3.400 63.051 92.471 6(BET1 4 OG1 -HG1 )(O -C 3 BET1) 0.000 3.800 63.438 108.106 7(BET1 4 OG1 -HG1 )(O -C 3 BET2) 0.000 4.462 78.291 67.190 8(BET1 4 OG1 -HG1 )(OD1 -CG 4 BET2) 0.000 3.530 57.674 88.997 9(BET1 4 OG1 -HG1 )(OD2 -CG 4 BET2) 0.000 4.411 21.493 114.693 10(BET1 5 N -H )(O -C 3 BET1) 0.000 4.383 85.102 89.377 11(BET1 5 N -H )(OG1 - 4 BET1) 0.000 4.474 88.565 0.000 12(BET1 5 N -H )(O -C 3 BET2) -2.148 2.901 18.097 29.883 13(BET1 6 N -H )(O -C 4 BET1) 0.000 4.328 88.058 88.217 14(BET1 7 N -H )(O -C 5 BET1) 0.000 4.289 78.980 89.949 15(BET1 7 ND1 -HD1 )(OT2 -C 7 BET1) 0.000 4.903 79.677 99.948 16(BET1 7 NE2 -HE2 )(OG1 - 3 BET2) -2.087 2.533 11.847 0.000 17(BET2 3 N -H )(O -C 5 BET1) -1.593 2.951 26.447 32.541 18(BET2 3 N -H )(O -C 3 BET2) 0.000 2.853 78.524 104.178 19(BET2 5 N -H )(O -C 3 BET1) -1.785 2.862 27.000 25.785 20(BET2 5 N -H )(O -C 3 BET2) 0.000 4.010 86.943 84.198 21(BET2 5 N -H )(OD1 -CG 4 BET2) 0.000 4.866 79.356 139.400 22(BET2 5 N -H )(OD2 -CG 4 BET2) 0.000 3.663 86.979 88.550 23(BET2 5 N -H )(O -C 5 BET2) 0.000 2.832 88.950 101.581 24(BET2 6 N -H )(O -C 4 BET2) 0.000 4.255 78.461 93.004 25(BET2 6 N -H )(O -C 6 BET2) 0.000 2.884 87.525 102.459 26(BET2 7 N -H )(O -C 5 BET2) 0.000 4.497 82.576 93.889 %X-PLOR-ERR: "END" not allowed. "STOP" terminates program X-PLOR>energy end --------------- cycle= 12 -------------------------------------------------- | Etotal =-14.315 grad(E)=1.039 E(HBON)=-14.315 | | Vpert =0.000 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>constraints ? end FIX : 0 atoms fixed INTE: 4 active double selections --------------- double selection 1 --------------------------------------- | WEIGhts : | | E(HBON)=1.000 | | VWEIghts : | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- double selection 2 --------------------------------------- | WEIGhts : | | E(HBON)=0.500 | | VWEIghts : | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- double selection 3 --------------------------------------- | WEIGhts : | | E(HBON)=0.500 | | VWEIghts : | | E(HBON)=0.000 | ------------------------------------------------------------------------------- --------------- double selection 4 --------------------------------------- | WEIGhts : | | E(HBON)=1.000 | | VWEIghts : | | E(HBON)=0.000 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>stop HEAP: maximum use= 641095 current use= 614370 X-PLOR: total CPU time= 0.0600 s X-PLOR: entry time at 15:21:08 11-Jun-07 X-PLOR: exit time at 15:21:09 11-Jun-07