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 10:27:30 X-PLOR>remarks ++++++++++++++++ HBONDTEST ++++++++++++++++++++++++++++++++++ X-PLOR>remarks Test run for the hydrogen position builder, the hydrogen bond X-PLOR>remarks selection routines , the hydrogen bond listings and the X-PLOR>remarks hydrogen bond I/O. X-PLOR>remarks by Axel Brunger 1982/83 X-PLOR> X-PLOR>rtf @TOPPAR:toph11.pro end ASSFIL: file /home/schwitrs/xplor/toppar/toph11.pro opened. RTFRDR>REMARKS TOPH11.PRO ( from TOPH10.INP) RTFRDR>REMARKS ============================= RTFRDR>REMARKS Charges and atom order modified for neutral GROUPs. RTFRDR>REMARKS Histidine charges set to Del Bene and Cohen sto-3g calculations. RTFRDR>REMARKS Amide charges set to match the experimental dipole moment. RTFRDR>REMARKS DNA/RNA atoms appended . RTFRDR>REMARKS few atoms never referenced switched off. RTFRDR>REMARKS Default for HIStidines is the doubly protonated state RTFRDR> RTFRDR>set echo=false end RTFRDR> end X-PLOR>parameter @TOPPAR:param11.pro end ASSFIL: file /home/schwitrs/xplor/toppar/param11.pro opened. PARRDR>REMARKS PARAM11.PRO ( from PARAM6A ) PARRDR>REMARKS =========== PARRDR>REMARKS PROTEIN PARAMETERS: PARRDR>REMARKS PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) PARRDR>REMARKS TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) PARRDR>REMARKS LENNARD-JONES NONBONDED PARAMETERS WITH SPECIAL TREATMENT OF 1:4 PARRDR>REMARKS CARBON-CARBON INTERACTIONS: JORGENSON ET. AL. PARRDR>REMARKS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 PARRDR>REMARKS PARRDR>set echo=false end PARRDR> end X-PLOR> X-PLOR>segment SEGMENT> name=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=4.5 aon=50.0 aoff=70. HBDSET> acut=90.0 tolerance=0.25 HBDSET> end PARRDR>end X-PLOR>print hbonds HBONDS: allocating space for 130 h-bond interactions. HBONDS: 613 distance exclusions and 49 angle exclusions HBONDS: 0 fixed h-bonds, currently 31 h-bonds present HBPRIN: list of 31 h-bond pairs HBOND ENERGY DISTANCE 180- A-H-D H-A-AA 1(BET1 2 N -H )(O -C 2 BET1) 0.000 2.748 76.732 95.878 2(BET1 3 N -H )(O -C 3 BET1) 0.000 2.846 76.787 98.950 3(BET1 3 N -H )(O -C 5 BET2) -1.740 2.990 25.593 29.403 4(BET1 3 ND2 -HD21)(O -C 3 BET1) 0.000 4.290 86.992 111.076 5(BET1 3 ND2 -HD22)(O -C 4 BET1) 0.000 3.852 83.777 69.722 6(BET1 4 N -H )(OD1 -CG 3 BET1) 0.000 3.400 63.051 92.471 7(BET1 4 OG1 -HG1 )(O -C 3 BET1) 0.000 3.800 63.438 108.106 8(BET1 4 OG1 -HG1 )(O -C 3 BET2) 0.000 4.462 78.291 67.190 9(BET1 4 OG1 -HG1 )(OD1 -CG 4 BET2) 0.000 3.530 57.674 88.997 10(BET1 4 OG1 -HG1 )(OD2 -CG 4 BET2) 0.000 4.411 21.493 114.693 11(BET1 5 N -H )(O -C 3 BET1) 0.000 4.383 85.102 89.377 12(BET1 5 N -H )(OG1 - 4 BET1) 0.000 4.474 88.565 0.000 13(BET1 5 N -H )(O -C 3 BET2) -2.148 2.901 18.097 29.883 14(BET1 6 N -H )(O -C 4 BET1) 0.000 4.328 88.058 88.217 15(BET1 7 N -H )(O -C 5 BET1) 0.000 4.289 78.980 89.949 16(BET1 7 N -H )(O -C 1 BET2) -2.577 2.993 7.746 28.510 17(BET1 7 NE2 -HE2 )(OG1 - 3 BET2) -2.087 2.533 11.847 0.000 18(BET2 1 N -HT2 )(O -C 1 BET2) 0.000 2.789 84.455 98.451 19(BET2 2 N -H )(O -C 2 BET2) 0.000 2.701 80.995 98.364 20(BET2 3 N -H )(O -C 5 BET1) -1.593 2.951 26.447 32.541 21(BET2 3 N -H )(O -C 3 BET2) 0.000 2.853 78.524 104.178 22(BET2 3 OG1 -HG1 )(O -C 2 BET2) 0.000 3.709 72.690 92.317 23(BET2 4 N -H )(O -C 2 BET2) 0.000 4.403 82.432 95.411 24(BET2 5 N -H )(O -C 3 BET1) -1.785 2.862 27.000 25.785 25(BET2 5 N -H )(O -C 3 BET2) 0.000 4.010 86.943 84.198 26(BET2 5 N -H )(OD2 -CG 4 BET2) 0.000 3.663 86.979 88.550 27(BET2 5 N -H )(O -C 5 BET2) 0.000 2.832 88.950 101.581 28(BET2 6 N -H )(O -C 4 BET2) 0.000 4.255 78.461 93.004 29(BET2 6 N -H )(O -C 6 BET2) 0.000 2.884 87.525 102.459 30(BET2 7 N -H )(O -C 1 BET1) -2.385 2.947 18.378 23.362 31(BET2 7 N -H )(O -C 5 BET2) 0.000 4.497 82.576 93.889 X-PLOR>! X-PLOR>! X-PLOR>! TEST CUTOFFS X-PLOR>parameter PARRDR> hbonds HBDSET> acceptor=true don=3.5 doff=4.0 dcut=4.5 HBDSET> aon=50.0 aoff=70.0 acut=45.0 tolerance=0.25 HBDSET> end PARRDR>end X-PLOR>print hbonds HBONDS: allocating space for 43 h-bond interactions. HBONDS: 613 distance exclusions and 72 angle exclusions HBONDS: 0 fixed h-bonds, currently 8 h-bonds present HBPRIN: list of 8 h-bond pairs HBOND ENERGY DISTANCE 180- A-H-D H-A-AA 1(BET1 3 N -H )(O -C 5 BET2) -1.740 2.990 25.593 29.403 2(BET1 4 OG1 -HG1 )(OD2 -CG 4 BET2) 0.000 4.411 21.493 114.693 3(BET1 5 N -H )(O -C 3 BET2) -2.148 2.901 18.097 29.883 4(BET1 7 N -H )(O -C 1 BET2) -2.577 2.993 7.746 28.510 5(BET1 7 NE2 -HE2 )(OG1 - 3 BET2) -2.087 2.533 11.847 0.000 6(BET2 3 N -H )(O -C 5 BET1) -1.593 2.951 26.447 32.541 7(BET2 5 N -H )(O -C 3 BET1) -1.785 2.862 27.000 25.785 8(BET2 7 N -H )(O -C 1 BET1) -2.385 2.947 18.378 23.362 X-PLOR>! X-PLOR>! X-PLOR>! TEST SWITCHING FUNCTIONS X-PLOR>parameter PARRDR> hbonds HBDSET> acceptor=true don=4.5 doff=4.5 dcut=5.0 HBDSET> aon=90.0 aoff=90.0 acut=90.0 tolerance=0.25 HBDSET> HBDSET> end PARRDR>end X-PLOR>print hbonds HBONDS: allocating space for 13 h-bond interactions. HBONDS: ran out of space. Starting over. 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>! X-PLOR>! TEST "FIXED" HYDROGEN BONDS X-PLOR>! X-PLOR>cons CONS> interaction=( not ( atom * * O* OR atom * * H* ) )=( all ) SELRPN: 90 atoms have been selected out of 143 SELRPN: 143 atoms have been selected out of 143 CONS>end X-PLOR> X-PLOR>parameter PARRDR> hbonds HBDSET> acceptor=true don=3.5 doff=4.0 dcut=4.5 HBDSET> aon=50.0 aoff=70.0 acut=90.0 tolerance=0.25 HBDSET> end PARRDR>end X-PLOR>print hbonds HBONDS: allocating space for 53 h-bond interactions. HBONDS: 607 distance exclusions and 49 angle exclusions HBONDS: 6 fixed h-bonds, currently 31 h-bonds present HBPRIN: list of 31 h-bond pairs HBOND ENERGY DISTANCE 180- A-H-D H-A-AA 1(BET1 2 N -H )(O -C 2 BET1) 0.000 2.748 76.732 95.878 2(BET1 3 N -H )(O -C 3 BET1) 0.000 2.846 76.787 98.950 3(BET1 3 N -H )(O -C 5 BET2) -1.740 2.990 25.593 29.403 4(BET1 3 ND2 -HD21)(O -C 3 BET1) 0.000 4.290 86.992 111.076 5(BET1 3 ND2 -HD22)(O -C 4 BET1) 0.000 3.852 83.777 69.722 6(BET1 4 N -H )(OD1 -CG 3 BET1) 0.000 3.400 63.051 92.471 7(BET1 4 OG1 -HG1 )(O -C 3 BET1) 0.000 3.800 63.438 108.106 8(BET1 4 OG1 -HG1 )(O -C 3 BET2) 0.000 4.462 78.291 67.190 9(BET1 4 OG1 -HG1 )(OD1 -CG 4 BET2) 0.000 3.530 57.674 88.997 10(BET1 4 OG1 -HG1 )(OD2 -CG 4 BET2) 0.000 4.411 21.493 114.693 11(BET1 5 N -H )(O -C 3 BET1) 0.000 4.383 85.102 89.377 12(BET1 5 N -H )(OG1 - 4 BET1) 0.000 4.474 88.565 0.000 13(BET1 5 N -H )(O -C 3 BET2) -2.148 2.901 18.097 29.883 14(BET1 6 N -H )(O -C 4 BET1) 0.000 4.328 88.058 88.217 15(BET1 7 N -H )(O -C 5 BET1) 0.000 4.289 78.980 89.949 16(BET1 7 N -H )(O -C 1 BET2) -2.577 2.993 7.746 28.510 17(BET1 7 NE2 -HE2 )(OG1 - 3 BET2) -2.087 2.533 11.847 0.000 18(BET2 1 N -HT2 )(O -C 1 BET2) 0.000 2.789 84.455 98.451 19(BET2 2 N -H )(O -C 2 BET2) 0.000 2.701 80.995 98.364 20(BET2 3 N -H )(O -C 5 BET1) -1.593 2.951 26.447 32.541 21(BET2 3 N -H )(O -C 3 BET2) 0.000 2.853 78.524 104.178 22(BET2 3 OG1 -HG1 )(O -C 2 BET2) 0.000 3.709 72.690 92.317 23(BET2 4 N -H )(O -C 2 BET2) 0.000 4.403 82.432 95.411 24(BET2 5 N -H )(O -C 3 BET1) -1.785 2.862 27.000 25.785 25(BET2 5 N -H )(O -C 3 BET2) 0.000 4.010 86.943 84.198 26(BET2 5 N -H )(OD2 -CG 4 BET2) 0.000 3.663 86.979 88.550 27(BET2 5 N -H )(O -C 5 BET2) 0.000 2.832 88.950 101.581 28(BET2 6 N -H )(O -C 4 BET2) 0.000 4.255 78.461 93.004 29(BET2 6 N -H )(O -C 6 BET2) 0.000 2.884 87.525 102.459 30(BET2 7 N -H )(O -C 1 BET1) -2.385 2.947 18.378 23.362 31(BET2 7 N -H )(O -C 5 BET2) 0.000 4.497 82.576 93.889 X-PLOR>! X-PLOR>stop HEAP: maximum use= 906168 current use= 873447 X-PLOR: total CPU time= 0.1600 s X-PLOR: entry time at 10:27:30 04-Jun-04 X-PLOR: exit time at 10:27:30 04-Jun-04