XPLOR-NIH version 2.9.5 C.D. Schwieters, J.J. Kuszewski, based on X-PLOR 3.851 by A.T. Brunger N. Tjandra, and G.M. Clore J. Magn. Res., 160, 66-74 (2003). http://nmr.cit.nih.gov/xplor-nih User: [unknown] on: x86/Linux at: 04-Jun-04 10:28:10 X-PLOR>REMARKS TEST.INP X-PLOR>REMARKS TEST OF THE PROTEIN SYSTEM USING PTI EXTENDED ATOM AND X-PLOR>REMARKS EXPLICIT HYDROGEN X-PLOR>REMARKS MODELS. WE USE A SHORTENED PTI TO SPEED THE RUN. X-PLOR> X-PLOR>rtf @TOPPAR:toph11.pro @TOPPAR:toph11.wat 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> @TOPPAR:toph11.wat end ASSFIL: file /home/schwitrs/xplor/toppar/toph11.wat opened. RTFRDR>remarks TOPH11.WAT RTFRDR>remarks ========== RTFRDR>remarks topology file for water RTFRDR>remarks available: TIP3P model RTFRDR> RTFRDR>set echo=false end RTFRDR> end X-PLOR>parameter @TOPPAR:param11.pro @TOPPAR:param11.wat 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> @TOPPAR:param11.wat end ASSFIL: file /home/schwitrs/xplor/toppar/param11.wat opened. PARRDR>remarks PARAM11.WAT (water parameters) PARRDR>remarks =========== PARRDR>remarks available: TIPS3P model PARRDR>set echo=false end PARRDR> end X-PLOR> X-PLOR>SEGMENT SEGMENT> NAME=M1 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 ARG PRO ASP PHE CYS LEU end MAPIC: Atom numbers being modified MAPIC: Atom numbers being modified CHAIN> END SEGMENT>END SEGMNT: 6 residues were inserted into segment "M1 " XPLOR: current counts (number in parenthesis is maximum) NATOM= 64(MAXA= 200) NBOND= 65(MAXB= 100) NTHETA= 93(MAXT= 100) NGRP= 22(MAXGRP= 100) NPHI= 39(MAXP= 100) NIMPHI= 28(MAXIMP= 100) NDON= 12(MAXPAD= 100) NACC= 9(MAXPAD= 100) NNB= 3(MAXNB= 100) X-PLOR> X-PLOR>SEGMENT SEGMENT> NAME=M2 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 CYS END MAPIC: Atom numbers being modified MAPIC: Atom numbers being modified CHAIN> END SEGMENT>END SEGMNT: 1 residues were inserted into segment "M2 " XPLOR: current counts (number in parenthesis is maximum) NATOM= 74(MAXA= 200) NBOND= 74(MAXB= 100) NTHETA= 106(MAXT= 200) NGRP= 25(MAXGRP= 100) NPHI= 44(MAXP= 100) NIMPHI= 30(MAXIMP= 100) NDON= 15(MAXPAD= 100) NACC= 11(MAXPAD= 100) NNB= 3(MAXNB= 100) X-PLOR> X-PLOR> X-PLOR>PATCH DISU REFERENCE 1 ( ATOM M1 5 * ) REFERENCE 2 ( ATOM M2 1 * ) END SELRPN: 7 atoms have been selected out of 74 SELRPN: 10 atoms have been selected out of 74 MAPIC: Atom numbers being modified XPLOR: current counts (number in parenthesis is maximum) NATOM= 74(MAXA= 200) NBOND= 75(MAXB= 100) NTHETA= 108(MAXT= 200) NGRP= 25(MAXGRP= 100) NPHI= 47(MAXP= 100) NIMPHI= 30(MAXIMP= 100) NDON= 15(MAXPAD= 100) NACC= 11(MAXPAD= 100) NNB= 3(MAXNB= 100) X-PLOR> X-PLOR>SEGMENT SEGMENT> NAME=SOLV SEGMENT> MOLECULE NAME=TIP3 NUMBER=1 END SEGMENT>END SEGMNT: 1 residues were inserted into segment "SOLV" XPLOR: current counts (number in parenthesis is maximum) NATOM= 77(MAXA= 200) NBOND= 77(MAXB= 100) NTHETA= 109(MAXT= 200) NGRP= 26(MAXGRP= 100) NPHI= 47(MAXP= 100) NIMPHI= 30(MAXIMP= 100) NDON= 15(MAXPAD= 100) NACC= 11(MAXPAD= 100) NNB= 3(MAXNB= 100) X-PLOR> X-PLOR>coor COOR> REMARKS COORDINATE FILE FOR MAIN TEST CASE "TEST" COOR> REMARKS COOR> REMARKS TEST OF THE PROTEIN SYSTEM USING PTI EXTENDED ATOM AND COOR> REMARKS EXPLICIT HYDROGEN COOR> REMARKS MODELS. WE USE A SHORTENED PTI TO SPEED THE RUN. COOR> COOR> NATOms = 60 COOR> 3 1 ARG N 26.52150 27.41672 -2.68671 M1 1 0.00000 %READC-ERR: still 17 missing coordinates (in selected subset) X-PLOR> X-PLOR>parameter PARRDR> nbonds NBDSET> NBXM=5 CDIE SHIFT VSWITCH NBDSET> CUTNB=100. CTONNB=98.0 CTOFNB=99.0 tolerance=0.5 NBDSET> end PARRDR> hbonds HBDSET> DCUT=10.5 DOFF=9.5 DON=9.0 tolerance=0.5 HBDSET> ACUT=180.0 AOFF=45.0 AON=25.0 HBDSET> end PARRDR>end X-PLOR> X-PLOR>hbuild HBUILD> selection=(hydrogen) SELRPN: 17 atoms have been selected out of 77 HBUILD>end HBUILD: dihedral PHI STePs for spin = 10.0000 HBUILD: cutoff during water acceptor search = 7.5000 HBUILD: HE , , placed for donor M1 1 ARG NE . HBUILD: H , , placed for donor M1 3 ASP N . HBUILD: H , , placed for donor M1 4 PHE N . HBUILD: H , , placed for donor M1 5 CYS N . HBUILD: H , , placed for donor M1 6 LEU N . MAKINB: mode 5 found 15 exclusions, 6 interactions(1-4) and 9 GB exclusions HBONDS: allocating space for 157 h-bond interactions. HBONDS: 9 distance exclusions and 0 angle exclusions HBONDS: 132 fixed h-bonds, currently 24 h-bonds present HBONDS: allocating space for 34 h-bond interactions. HBONDS: 9 distance exclusions and 0 angle exclusions HBONDS: 132 fixed h-bonds, currently 24 h-bonds present HBONDS: allocating space for 34 h-bond interactions. HBONDS: 9 distance exclusions and 0 angle exclusions HBONDS: 132 fixed h-bonds, currently 24 h-bonds present HBONDS: allocating space for 34 h-bond interactions. HBONDS: 9 distance exclusions and 0 angle exclusions HBONDS: 132 fixed h-bonds, currently 24 h-bonds present HBUILD: HT1 ,HT2 ,HT3 , constructed (spin) for donor M1 1 ARG N . MAKINB: mode 5 found 9 exclusions, 4 interactions(1-4) and 5 GB exclusions HBONDS: allocating space for 34 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 143 fixed h-bonds, currently 22 h-bonds present HBONDS: allocating space for 31 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 143 fixed h-bonds, currently 22 h-bonds present HBONDS: allocating space for 31 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 143 fixed h-bonds, currently 22 h-bonds present HBONDS: allocating space for 31 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 143 fixed h-bonds, currently 22 h-bonds present HBONDS: allocating space for 31 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 143 fixed h-bonds, currently 22 h-bonds present HBUILD: HH11,HH12, , constructed (spin) for donor M1 1 ARG NH1 . MAKINB: mode 5 found 9 exclusions, 4 interactions(1-4) and 5 GB exclusions HBONDS: allocating space for 31 h-bond interactions. HBONDS: 8 distance exclusions and 0 angle exclusions HBONDS: 143 fixed h-bonds, currently 14 h-bonds present HBONDS: allocating space for 21 h-bond interactions. HBONDS: 8 distance exclusions and 0 angle exclusions HBONDS: 143 fixed h-bonds, currently 14 h-bonds present HBONDS: allocating space for 21 h-bond interactions. HBONDS: 8 distance exclusions and 0 angle exclusions HBONDS: 143 fixed h-bonds, currently 14 h-bonds present HBONDS: allocating space for 21 h-bond interactions. HBONDS: 8 distance exclusions and 0 angle exclusions HBONDS: 143 fixed h-bonds, currently 14 h-bonds present HBONDS: allocating space for 21 h-bond interactions. HBONDS: 8 distance exclusions and 0 angle exclusions HBONDS: 143 fixed h-bonds, currently 14 h-bonds present HBUILD: HH21,HH22, , constructed (spin) for donor M1 1 ARG NH2 . MAKINB: mode 5 found 15 exclusions, 6 interactions(1-4) and 9 GB exclusions HBONDS: allocating space for 21 h-bond interactions. HBONDS: 12 distance exclusions and 0 angle exclusions HBONDS: 132 fixed h-bonds, currently 21 h-bonds present HBONDS: allocating space for 30 h-bond interactions. HBONDS: 12 distance exclusions and 0 angle exclusions HBONDS: 132 fixed h-bonds, currently 21 h-bonds present HBONDS: allocating space for 30 h-bond interactions. HBONDS: 12 distance exclusions and 0 angle exclusions HBONDS: 132 fixed h-bonds, currently 21 h-bonds present HBONDS: allocating space for 30 h-bond interactions. HBONDS: 12 distance exclusions and 0 angle exclusions HBONDS: 132 fixed h-bonds, currently 21 h-bonds present HBUILD: HT1 ,HT2 ,HT3 , constructed (spin) for donor M2 1 CYS N . MAKINB: mode 5 found 3 exclusions, 0 interactions(1-4) and 3 GB exclusions HBONDS: allocating space for 30 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 165 fixed h-bonds, currently 0 h-bonds present HBONDS: allocating space for 157 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 165 fixed h-bonds, currently 0 h-bonds present HBONDS: allocating space for 157 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 165 fixed h-bonds, currently 0 h-bonds present HBONDS: allocating space for 157 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 165 fixed h-bonds, currently 0 h-bonds present HBONDS: allocating space for 157 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 165 fixed h-bonds, currently 0 h-bonds present HBONDS: allocating space for 157 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 165 fixed h-bonds, currently 0 h-bonds present HBONDS: allocating space for 157 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 165 fixed h-bonds, currently 0 h-bonds present HBONDS: allocating space for 157 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 165 fixed h-bonds, currently 0 h-bonds present HBONDS: allocating space for 157 h-bond interactions. HBONDS: 0 distance exclusions and 0 angle exclusions HBONDS: 165 fixed h-bonds, currently 0 h-bonds present HBUILD:H1 ,H2 , , constructed for water SOLV 1 TIP3 HBUILD: Minimum distance between water and solute is 2.86943 A. X-PLOR> X-PLOR>parameter !! for normal h-bond evaluation PARRDR> HBONDS HBDSET> DCUT=10.0 DOFF=9.5 DON=9.0 HBDSET> ACUT=65.0 AOFF=45.0 AON=25.0 tolerance=0.5 HBDSET> END %HBDSET-ERR: inconsistent DCUT, TOLErance, DOFF given. Reset. PARRDR> nbonds NBDSET> tolerance=0.5 NBDSET> end PARRDR>end X-PLOR> X-PLOR>PRINT HBONDS HBONDS: allocating space for 157 h-bond interactions. HBONDS: 31 distance exclusions and 109 angle exclusions HBONDS: 0 fixed h-bonds, currently 25 h-bonds present HBPRIN: list of 25 h-bond pairs HBOND ENERGY DISTANCE 180- A-H-D H-A-AA 1(M1 1 NE -HE )(OT1 -C 1 M2 ) -1.986 2.795 25.098 21.998 2(M1 1 NE -HE )(OT2 -C 1 M2 ) 0.000 4.850 17.682 137.696 3(M1 1 NH1 -HH11)(O -C 1 M1 ) 0.000 5.709 56.194 80.538 4(M1 1 NH1 -HH11)(O -C 2 M1 ) -0.003 6.604 41.845 51.790 5(M1 1 NH1 -HH11)(OD1 -CG 3 M1 ) -0.064 8.370 20.785 39.351 6(M1 1 NH1 -HH11)(OD2 -CG 3 M1 ) 0.000 10.411 17.327 152.770 7(M1 1 NH1 -HH11)(O -C 3 M1 ) 0.000 8.713 22.765 89.304 8(M1 1 NH1 -HH11)(O -C 4 M1 ) 0.000 10.364 46.321 129.847 9(M1 1 NH1 -HH11)(O -C 5 M1 ) 0.000 7.609 61.957 103.057 10(M1 1 NH1 -HH11)(OT1 -C 6 M1 ) 0.000 9.864 47.004 118.075 11(M1 1 NH1 -HH11)(OT2 -C 6 M1 ) 0.000 10.222 43.056 131.987 12(M1 1 NH2 -HH21)(OT1 -C 1 M2 ) 0.000 4.035 59.279 44.869 13(M1 1 NH2 -HH21)(OT2 -C 1 M2 ) 0.000 5.487 35.809 108.894 14(M1 1 N -HT1 )(OD1 -CG 3 M1 ) 0.000 7.533 63.371 39.019 15(M1 1 N -HT3 )(OT2 -C 1 M2 ) 0.000 6.447 58.371 114.286 16(M1 5 N -H )(O -C 1 M1 ) 0.000 6.291 29.514 107.137 17(M1 5 N -H )(O -C 2 M1 ) -0.105 3.211 32.667 72.431 18(M1 5 N -H )(OD1 -CG 3 M1 ) 0.000 6.849 47.694 101.693 19(M1 5 N -H )(OD2 -CG 3 M1 ) 0.000 7.703 54.159 155.046 20(M1 6 N -H )(O -C 1 M1 ) 0.000 7.202 59.605 88.842 21(M1 6 N -H )(O -C 2 M1 ) 0.000 4.481 54.739 50.645 22(M1 6 N -H )(OD1 -CG 3 M1 ) 0.000 7.043 33.363 99.766 23(M1 6 N -H )(OD2 -CG 3 M1 ) 0.000 8.010 23.160 147.997 24(M1 6 N -H )(O -C 3 M1 ) -0.512 3.142 17.353 64.361 25(M2 1 N -HT3 )(O -C 4 M1 ) 0.000 8.829 54.900 113.406 X-PLOR> X-PLOR>SHAKE SHAKE> MOLECULE ( RESNAME TIP3 ) SELRPN: 3 atoms have been selected out of 77 SHKSET: reference = coordinates SHAKE>END X-PLOR> X-PLOR> X-PLOR>parameter PARRDR> NBONDS NBDSET> NBXM=5 CDIE SHIFT VSWITCH WMIN 2.0 NBDSET> CUTNB=8 CTOFNB=7.5 CTONNB=7.0 tolerance=0.5 NBDSET> END %NBDSET-ERR: inconsistent CUTNB, TOLErance, CTOFNB given. Reset. PARRDR> HBONDS HBDSET> DCUT=4.5 DOFF=4.0 DON=3.5 HBDSET> ACUT=65.0 AOFF=50.0 AON=40.0 HBDSET> END %HBDSET-ERR: inconsistent DCUT, TOLErance, DOFF given. Reset. PARRDR>end X-PLOR> X-PLOR>set seed=31459.0 end X-PLOR> X-PLOR>DYNAMICS VERLET DYNAmics> trajectory=test.dat DYNAmics> NSTEP=10 TIME=0.0009778 DYNAmics> IHTFRQ=500 NTRFRQ=5 DYNAmics> FIRSTT=0.0 FINALT=300.0 TWINDH=3.0 TWINDL=1.0 DYNAmics> IPRFRQ=5 NPRINT=1 NSAVC=1 DYNAmics>END ASSFIL: file test.dat opened. DYNAMC: number of degrees of freedom= 228 ASSVEL: zero velocities CENMAS: Information about center of free masses position [A] : 24.03807 23.34724 0.59493 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 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 24.03807 23.34724 0.59493 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 SHAKEA: coordinates SHAKEd in 1 iterations. MAKINB: mode 5 found 309 exclusions, 120 interactions(1-4) and 189 GB exclusions %atoms "M1 -1 -ARG -HE " and "M2 -1 -CYS -OT1 " only 1.88 A apart HBONDS: allocating space for 35 h-bond interactions. HBONDS: 133 distance exclusions and 26 angle exclusions HBONDS: 0 fixed h-bonds, currently 6 h-bonds present --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=-54.914 E(kin)=0.000 temperature=0.000 | | Etotal =-54.914 grad(E)=20.380 E(BOND)=16.643 E(ANGL)=12.861 | | E(DIHE)=13.963 E(IMPR)=1.112 E(VDW )=-10.679 E(ELEC)=-86.170 | | E(HBON)=-2.644 | ------------------------------------------------------------------------------- SHAKEA: coordinates SHAKEd in 15 iterations. WRITEC: CORD sets starting from step 1 are written every 1 steps WRITEC: where 77 atoms are "free" SHAKEA: coordinates SHAKEd in 16 iterations. --------------- step= 1 at 0.00098 ps -------------------------------- | E(kin)+E(total)=-54.948 E(kin)=1.509 temperature=6.660 | | Etotal =-56.456 grad(E)=19.597 E(BOND)=15.597 E(ANGL)=12.677 | | E(DIHE)=13.952 E(IMPR)=1.100 E(VDW )=-10.759 E(ELEC)=-86.364 | | E(HBON)=-2.660 | ------------------------------------------------------------------------------- SHAKEA: coordinates SHAKEd in 16 iterations. --------------- step= 2 at 0.00196 ps -------------------------------- | E(kin)+E(total)=-55.030 E(kin)=5.539 temperature=24.451 | | Etotal =-60.570 grad(E)=17.378 E(BOND)=12.864 E(ANGL)=12.190 | | E(DIHE)=13.920 E(IMPR)=1.068 E(VDW )=-10.991 E(ELEC)=-86.915 | | E(HBON)=-2.706 | ------------------------------------------------------------------------------- SHAKEA: coordinates SHAKEd in 16 iterations. --------------- step= 3 at 0.00293 ps -------------------------------- | E(kin)+E(total)=-55.126 E(kin)=10.841 temperature=47.857 | | Etotal =-65.967 grad(E)=14.111 E(BOND)=9.446 E(ANGL)=11.567 | | E(DIHE)=13.868 E(IMPR)=1.030 E(VDW )=-11.356 E(ELEC)=-87.742 | | E(HBON)=-2.780 | ------------------------------------------------------------------------------- SHAKEA: coordinates SHAKEd in 16 iterations. --------------- step= 4 at 0.00391 ps -------------------------------- | E(kin)+E(total)=-55.200 E(kin)=15.961 temperature=70.455 | | Etotal =-71.161 grad(E)=10.521 E(BOND)=6.458 E(ANGL)=11.013 | | E(DIHE)=13.801 E(IMPR)=1.007 E(VDW )=-11.827 E(ELEC)=-88.733 | | E(HBON)=-2.879 | ------------------------------------------------------------------------------- SHAKEA: coordinates SHAKEd in 16 iterations. --------------- step= 5 at 0.00489 ps -------------------------------- | E(kin)+E(total)=-55.237 E(kin)=19.745 temperature=87.159 | | Etotal =-74.982 grad(E)=8.003 E(BOND)=4.721 E(ANGL)=10.700 | | E(DIHE)=13.722 E(IMPR)=1.022 E(VDW )=-12.373 E(ELEC)=-89.775 | | E(HBON)=-2.998 | ------------------------------------------------------------------------------- --------------- averages for last 5 steps ----------------------------- | E(kin)+E(total)=-55.108 E(kin)=10.719 temperature=47.316 | | Etotal =-65.827 grad(E)=13.922 E(BOND)=9.817 E(ANGL)=11.629 | | E(DIHE)=13.852 E(IMPR)=1.045 E(VDW )=-11.461 E(ELEC)=-87.906 | | E(HBON)=-2.805 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 5 steps ----------------------- | E(kin)+E(total)=0.107 E(kin)=6.643 temperature=29.322 | | Etotal =6.749 grad(E)=4.261 E(BOND)=4.002 E(ANGL)=0.729 | | E(DIHE)=0.083 E(IMPR)=0.034 E(VDW )=0.582 E(ELEC)=1.230 | | E(HBON)=0.122 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 24.03807 23.34724 0.59493 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 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 24.03807 23.34724 0.59493 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 SHAKEA: coordinates SHAKEd in 1 iterations. --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=-55.237 E(kin)=19.745 temperature=87.159 | | Etotal =-74.982 grad(E)=8.003 E(BOND)=4.721 E(ANGL)=10.700 | | E(DIHE)=13.722 E(IMPR)=1.022 E(VDW )=-12.373 E(ELEC)=-89.775 | | E(HBON)=-2.998 | ------------------------------------------------------------------------------- SHAKEA: coordinates SHAKEd in 15 iterations. SHAKEA: coordinates SHAKEd in 16 iterations. --------------- step= 6 at 0.00587 ps -------------------------------- | E(kin)+E(total)=-55.234 E(kin)=21.610 temperature=95.392 | | Etotal =-76.844 grad(E)=8.410 E(BOND)=4.598 E(ANGL)=10.702 | | E(DIHE)=13.635 E(IMPR)=1.101 E(VDW )=-12.964 E(ELEC)=-90.788 | | E(HBON)=-3.128 | ------------------------------------------------------------------------------- SHAKEA: coordinates SHAKEd in 16 iterations. --------------- step= 7 at 0.00684 ps -------------------------------- | E(kin)+E(total)=-55.194 E(kin)=21.598 temperature=95.337 | | Etotal =-76.791 grad(E)=11.154 E(BOND)=5.990 E(ANGL)=10.981 | | E(DIHE)=13.543 E(IMPR)=1.265 E(VDW )=-13.571 E(ELEC)=-91.739 | | E(HBON)=-3.261 | ------------------------------------------------------------------------------- SHAKEA: coordinates SHAKEd in 16 iterations. --------------- step= 8 at 0.00782 ps -------------------------------- | E(kin)+E(total)=-55.125 E(kin)=20.332 temperature=89.750 | | Etotal =-75.457 grad(E)=14.264 E(BOND)=8.365 E(ANGL)=11.404 | | E(DIHE)=13.449 E(IMPR)=1.530 E(VDW )=-14.174 E(ELEC)=-92.643 | | E(HBON)=-3.387 | ------------------------------------------------------------------------------- SHAKEA: coordinates SHAKEd in 16 iterations. --------------- step= 9 at 0.00880 ps -------------------------------- | E(kin)+E(total)=-55.051 E(kin)=18.863 temperature=83.264 | | Etotal =-73.914 grad(E)=16.660 E(BOND)=10.845 E(ANGL)=11.792 | | E(DIHE)=13.352 E(IMPR)=1.904 E(VDW )=-14.758 E(ELEC)=-93.549 | | E(HBON)=-3.499 | ------------------------------------------------------------------------------- SHAKEA: coordinates SHAKEd in 16 iterations. --------------- step= 10 at 0.00978 ps -------------------------------- | E(kin)+E(total)=-55.004 E(kin)=18.309 temperature=80.819 | | Etotal =-73.313 grad(E)=17.841 E(BOND)=12.471 E(ANGL)=11.987 | | E(DIHE)=13.252 E(IMPR)=2.388 E(VDW )=-15.313 E(ELEC)=-94.509 | | E(HBON)=-3.591 | ------------------------------------------------------------------------------- --------------- averages for last 5 steps ----------------------------- | E(kin)+E(total)=-55.122 E(kin)=20.142 temperature=88.912 | | Etotal =-75.264 grad(E)=13.666 E(BOND)=8.454 E(ANGL)=11.373 | | E(DIHE)=13.446 E(IMPR)=1.638 E(VDW )=-14.156 E(ELEC)=-92.646 | | E(HBON)=-3.373 | ------------------------------------------------------------------------------- --------------- rms fluctations for last 5 steps ----------------------- | E(kin)+E(total)=0.085 E(kin)=1.364 temperature=6.023 | | Etotal =1.449 grad(E)=3.484 E(BOND)=2.926 E(ANGL)=0.481 | | E(DIHE)=0.135 E(IMPR)=0.463 E(VDW )=0.832 E(ELEC)=1.308 | | E(HBON)=0.165 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 24.03807 23.34724 0.59493 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>COOR COPY END COOR: selected main coordinates copied to comp X-PLOR> X-PLOR>CLOSE test.dat END %X-PLOR>-ERR: File test.dat was not open. X-PLOR> X-PLOR>DYNAMICS ANALYSIS AVERAGE AVECOR> input=test.dat BEGIN=1 SKIP=1 STOP=10 ASSFIL: file test.dat opened. AVECOR>END REMARKS FILENAME="test.dat" REMARKS COORDINATE FILE FOR MAIN TEST CASE "TEST" REMARKS REMARKS TEST OF THE PROTEIN SYSTEM USING PTI EXTENDED ATOM AND REMARKS EXPLICIT HYDROGEN REMARKS MODELS. WE USE A SHORTENED PTI TO SPEED THE RUN. REMARKS DATE:04-Jun-04 10:28:10 created by user: [unknown] READC: reading file= 1 ISTART= 1 READC: 77 atoms were "free" READC: NUNIt= 1 READC: BEGIn= 1 SKIP= 1 STOP= 10 READC: TIMEstep= 0.00097780 ps header= CORD READC: complete. 10 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="OUTPUT" REMARK COORDINATE FILE FOR MAIN TEST CASE "TEST" REMARK TEST OF THE PROTEIN SYSTEM USING PTI EXTENDED ATOM AND REMARK EXPLICIT HYDROGEN REMARK MODELS. WE USE A SHORTENED PTI TO SPEED THE RUN. REMARK DATE:04-Jun-04 10:28:10 created by user: [unknown] ATOM 1 HT1 ARG 1 27.090 26.628 -3.059 1.00 0.02 M1 ATOM 2 HT2 ARG 1 27.169 28.112 -2.263 1.00 0.01 M1 ATOM 3 N ARG 1 26.520 27.413 -2.682 1.00 0.00 M1 ATOM 4 HT3 ARG 1 25.980 27.868 -3.447 1.00 0.01 M1 ATOM 5 CA ARG 1 25.602 26.903 -1.670 1.00 0.01 M1 ATOM 6 CB ARG 1 24.614 25.886 -2.249 1.00 0.00 M1 ATOM 7 CG ARG 1 25.166 24.457 -2.387 1.00 0.01 M1 ATOM 8 CD ARG 1 24.120 23.542 -2.985 1.00 0.01 M1 ATOM 9 NE ARG 1 23.651 24.055 -4.274 1.00 0.00 M1 ATOM 10 HE ARG 1 22.787 24.556 -4.233 1.00 0.04 M1 ATOM 11 CZ ARG 1 24.295 23.859 -5.424 1.00 0.01 M1 ATOM 12 NH1 ARG 1 25.430 23.156 -5.475 1.00 0.00 M1 ATOM 13 HH11 ARG 1 25.800 22.741 -4.645 1.00 0.02 M1 ATOM 14 HH12 ARG 1 25.900 23.005 -6.342 1.00 0.01 M1 ATOM 15 NH2 ARG 1 23.798 24.380 -6.537 1.00 0.00 M1 ATOM 16 HH21 ARG 1 22.939 24.904 -6.500 1.00 0.01 M1 ATOM 17 HH22 ARG 1 24.243 24.254 -7.419 1.00 0.02 M1 ATOM 18 C ARG 1 26.259 26.227 -0.471 1.00 0.01 M1 ATOM 19 O ARG 1 27.268 25.529 -0.614 1.00 0.01 M1 ATOM 20 N PRO 2 25.676 26.421 0.711 1.00 0.01 M1 ATOM 21 CD PRO 2 24.634 27.415 0.968 1.00 0.01 M1 ATOM 22 CA PRO 2 26.202 25.813 1.914 1.00 0.01 M1 ATOM 23 CB PRO 2 25.358 26.402 3.017 1.00 0.01 M1 ATOM 24 CG PRO 2 24.537 27.554 2.476 1.00 0.01 M1 ATOM 25 C PRO 2 26.241 24.287 1.842 1.00 0.01 M1 ATOM 26 O PRO 2 25.460 23.661 1.116 1.00 0.00 M1 ATOM 27 N ASP 3 27.174 23.700 2.580 1.00 0.01 M1 ATOM 28 H ASP 3 27.837 24.232 3.064 1.00 0.05 M1 ATOM 29 CA ASP 3 27.300 22.246 2.638 1.00 0.00 M1 ATOM 30 CB ASP 3 28.492 21.856 3.497 1.00 0.01 M1 ATOM 31 CG ASP 3 29.788 21.834 2.717 1.00 0.01 M1 ATOM 32 OD1 ASP 3 29.874 22.174 1.545 1.00 0.01 M1 ATOM 33 OD2 ASP 3 30.771 21.490 3.327 1.00 0.01 M1 ATOM 34 C ASP 3 26.096 21.477 3.150 1.00 0.01 M1 ATOM 35 O ASP 3 25.829 20.343 2.765 1.00 0.01 M1 ATOM 36 N PHE 4 25.343 22.131 4.040 1.00 0.01 M1 ATOM 37 H PHE 4 25.609 23.041 4.264 1.00 0.03 M1 ATOM 38 CA PHE 4 24.190 21.498 4.661 1.00 0.00 M1 ATOM 39 CB PHE 4 23.778 22.286 5.890 1.00 0.01 M1 ATOM 40 CG PHE 4 23.256 23.680 5.602 1.00 0.01 M1 ATOM 41 CD1 PHE 4 22.028 23.838 4.996 1.00 0.02 M1 ATOM 42 CD2 PHE 4 23.937 24.813 5.978 1.00 0.01 M1 ATOM 43 CE1 PHE 4 21.504 25.076 4.716 1.00 0.01 M1 ATOM 44 CE2 PHE 4 23.381 26.063 5.735 1.00 0.02 M1 ATOM 45 CZ PHE 4 22.179 26.210 5.079 1.00 0.01 M1 ATOM 46 C PHE 4 23.010 21.338 3.707 1.00 0.02 M1 ATOM 47 O PHE 4 22.030 20.667 3.995 1.00 0.00 M1 ATOM 48 N CYS 5 23.106 22.047 2.578 1.00 0.01 M1 ATOM 49 H CYS 5 23.830 22.695 2.483 1.00 0.02 M1 ATOM 50 CA CYS 5 22.169 21.829 1.484 1.00 0.00 M1 ATOM 51 CB CYS 5 22.343 22.863 0.397 1.00 0.00 M1 ATOM 52 SG CYS 5 22.121 24.592 0.905 1.00 0.00 M1 ATOM 53 C CYS 5 22.197 20.461 0.807 1.00 0.01 M1 ATOM 54 O CYS 5 21.261 20.086 0.097 1.00 0.00 M1 ATOM 55 N LEU 6 23.292 19.737 1.014 1.00 0.01 M1 ATOM 56 H LEU 6 24.020 20.067 1.573 1.00 0.05 M1 ATOM 57 CA LEU 6 23.422 18.377 0.486 1.00 0.01 M1 ATOM 58 CB LEU 6 24.878 18.082 0.128 1.00 0.00 M1 ATOM 59 CG LEU 6 25.592 19.032 -0.805 1.00 0.00 M1 ATOM 60 CD1 LEU 6 26.956 18.478 -1.142 1.00 0.00 M1 ATOM 61 CD2 LEU 6 24.793 19.236 -2.073 1.00 0.00 M1 ATOM 62 C LEU 6 22.945 17.237 1.405 1.00 0.03 M1 ATOM 63 OT1 LEU 6 22.952 16.072 0.931 1.00 0.01 M1 ATOM 64 OT2 LEU 6 22.597 17.532 2.560 1.00 0.02 M1 ATOM 65 HT1 CYS 1 18.995 27.804 -1.198 1.00 0.03 M2 ATOM 66 HT2 CYS 1 20.467 28.612 -1.147 1.00 0.03 M2 ATOM 67 N CYS 1 19.975 27.746 -0.861 1.00 0.01 M2 ATOM 68 HT3 CYS 1 20.005 27.616 0.170 1.00 0.01 M2 ATOM 69 CA CYS 1 20.611 26.597 -1.504 1.00 0.01 M2 ATOM 70 CB CYS 1 19.915 25.341 -1.032 1.00 0.01 M2 ATOM 71 SG CYS 1 20.136 24.923 0.719 1.00 0.00 M2 ATOM 72 C CYS 1 20.728 26.487 -3.044 1.00 0.03 M2 ATOM 73 OT1 CYS 1 21.370 25.510 -3.515 1.00 0.01 M2 ATOM 74 OT2 CYS 1 20.181 27.366 -3.722 1.00 0.03 M2 ATOM 75 OH2 TIP3 1 21.418 27.233 -7.177 1.00 0.00 SOLV ATOM 76 H1 TIP3 1 21.071 27.254 -6.286 1.00 0.02 SOLV ATOM 77 H2 TIP3 1 21.029 27.996 -7.605 1.00 0.01 SOLV END X-PLOR> X-PLOR>COOR SWAP END COOR: selected coordinates swaped (main<->comp) X-PLOR> X-PLOR>MINIMIZE POWELL POWELL> NSTEP=2 STEP=50.0 POWELL>END POWELL: number of degrees of freedom= 231 SHAKEA: coordinates SHAKEd in 1 iterations. SHAKEF: forces SHAKEd in 15 iterations. --------------- cycle= 1 ------ stepsize= 0.0000 ----------------------- | Etotal =-73.313 grad(E)=17.841 E(BOND)=12.471 E(ANGL)=11.987 | | E(DIHE)=13.252 E(IMPR)=2.388 E(VDW )=-15.313 E(ELEC)=-94.509 | | E(HBON)=-3.591 | ------------------------------------------------------------------------------- SHAKEA: coordinates SHAKEd in 4 iterations. SHAKEF: forces SHAKEd in 15 iterations. --------------- cycle= 2 ------ stepsize= 0.0007 ----------------------- | Etotal =-75.080 grad(E)=18.959 E(BOND)=10.865 E(ANGL)=12.228 | | E(DIHE)=13.014 E(IMPR)=2.132 E(VDW )=-15.324 E(ELEC)=-94.417 | | E(HBON)=-3.578 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>PRINT HBONDS HBPRIN: list of 6 h-bond pairs HBOND ENERGY DISTANCE 180- A-H-D H-A-AA 1(M1 1 NE -HE )(OT1 -C 1 M2 ) -2.587 2.853 17.673 18.448 2(M1 1 NE -HE )(OT2 -C 1 M2 ) 0.000 4.843 18.617 138.333 3(M1 1 NH2 -HH21)(OT1 -C 1 M2 ) 0.000 4.054 57.804 41.471 4(M1 5 N -H )(O -C 2 M1 ) -0.187 3.209 29.666 71.286 5(M1 6 N -H )(O -C 2 M1 ) 0.000 4.492 63.556 51.300 6(M1 6 N -H )(O -C 3 M1 ) -0.804 3.133 10.484 59.332 X-PLOR> X-PLOR>close test.dat end X-PLOR>open test.dat access=append end close test.dat disp=delete end ASSFIL: file test.dat opened. X-PLOR> X-PLOR>STOP HEAP: maximum use= 918878 current use= 874432 X-PLOR: total CPU time= 0.1800 s X-PLOR: entry time at 10:28:10 04-Jun-04 X-PLOR: exit time at 10:28:10 04-Jun-04