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 15:33:20 X-PLOR>remarks TESTFIRS.INP X-PLOR>remarks test the analytic first derivatives for standard potentials 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=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>{* c-dielectric, shifting *} X-PLOR>{* ====================== *} X-PLOR>parameter PARRDR> hbonds HBDSET> acceptor=true don=4.7 doff=5.2 dcut=5.7 aon=50.0 aoff=70.0 acut=90.0 HBDSET> end %HBDSET-ERR: inconsistent DCUT, TOLErance, DOFF given. Reset. PARRDR> nbonds NBDSET> atom cdie shift eps=1.0 NBDSET> cutnb=30.0 ctonnb=6.0 ctofnb=8.0 NBDSET> nbxmod=5 vswitch NBDSET> end PARRDR>end X-PLOR> X-PLOR> X-PLOR>test first selection= ( all ) step=0.000001 tol=0.0 end SELRPN: 19 atoms have been selected out of 19 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 TESTFD: Parameters: STEP= 0.00000 MASSweighting=F TESTFD: The following first derivatives differ by more than TOL= 0.000000 DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 1 X ( TRYP 1 TRP HT1 ) 1.479092 1.479092 0.000000 1 Y ( TRYP 1 TRP HT1 ) -8.467564 -8.467564 0.000000 1 Z ( TRYP 1 TRP HT1 ) -5.718580 -5.718580 0.000000 2 X ( TRYP 1 TRP HT2 ) 6.398349 6.398349 0.000000 2 Y ( TRYP 1 TRP HT2 ) -3.044631 -3.044631 0.000000 2 Z ( TRYP 1 TRP HT2 ) -4.144821 -4.144821 0.000000 3 X ( TRYP 1 TRP N ) -13.317048 -13.317048 0.000000 3 Y ( TRYP 1 TRP N ) -16.116270 -16.116270 0.000000 3 Z ( TRYP 1 TRP N ) -26.097968 -26.097968 0.000000 4 X ( TRYP 1 TRP HT3 ) 2.849424 2.849424 0.000000 4 Y ( TRYP 1 TRP HT3 ) -5.571498 -5.571498 0.000000 4 Z ( TRYP 1 TRP HT3 ) -2.034637 -2.034637 0.000000 5 X ( TRYP 1 TRP CA ) 15.998273 15.998273 0.000000 5 Y ( TRYP 1 TRP CA ) 7.006924 7.006924 0.000000 5 Z ( TRYP 1 TRP CA ) 25.599286 25.599286 0.000000 6 X ( TRYP 1 TRP CB ) -6.518070 -6.518070 0.000000 6 Y ( TRYP 1 TRP CB ) 5.476678 5.476678 0.000000 6 Z ( TRYP 1 TRP CB ) 2.995732 2.995732 0.000000 7 X ( TRYP 1 TRP CG ) -7.004964 -7.004964 0.000000 7 Y ( TRYP 1 TRP CG ) 2.006184 2.006184 0.000000 7 Z ( TRYP 1 TRP CG ) -14.236944 -14.236944 0.000000 8 X ( TRYP 1 TRP CD2 ) 30.671756 30.671756 0.000000 8 Y ( TRYP 1 TRP CD2 ) -22.826804 -22.826804 0.000000 8 Z ( TRYP 1 TRP CD2 ) 7.168435 7.168435 0.000000 9 X ( TRYP 1 TRP CE2 ) -24.516741 -24.516741 0.000000 9 Y ( TRYP 1 TRP CE2 ) 6.789212 6.789212 0.000000 9 Z ( TRYP 1 TRP CE2 ) 14.272936 14.272936 0.000000 10 X ( TRYP 1 TRP CE3 ) -16.278745 -16.278745 0.000000 10 Y ( TRYP 1 TRP CE3 ) 11.385772 11.385772 0.000000 10 Z ( TRYP 1 TRP CE3 ) 9.915522 9.915522 0.000000 11 X ( TRYP 1 TRP CD1 ) -5.184037 -5.184037 0.000000 11 Y ( TRYP 1 TRP CD1 ) -9.851758 -9.851758 0.000000 11 Z ( TRYP 1 TRP CD1 ) 1.317201 1.317201 0.000000 12 X ( TRYP 1 TRP NE1 ) 30.250043 30.250043 0.000000 12 Y ( TRYP 1 TRP NE1 ) 20.564619 20.564619 0.000000 12 Z ( TRYP 1 TRP NE1 ) -30.276184 -30.276184 0.000000 13 X ( TRYP 1 TRP HE1 ) -15.804655 -15.804655 0.000000 13 Y ( TRYP 1 TRP HE1 ) -9.773541 -9.773541 0.000000 13 Z ( TRYP 1 TRP HE1 ) -1.019016 -1.019016 0.000000 14 X ( TRYP 1 TRP CZ2 ) 9.166841 9.166841 0.000000 14 Y ( TRYP 1 TRP CZ2 ) -3.087236 -3.087236 0.000000 14 Z ( TRYP 1 TRP CZ2 ) 14.929255 14.929255 0.000000 15 X ( TRYP 1 TRP CZ3 ) -2.667623 -2.667623 0.000000 15 Y ( TRYP 1 TRP CZ3 ) 1.430240 1.430240 0.000000 15 Z ( TRYP 1 TRP CZ3 ) -2.070128 -2.070128 0.000000 16 X ( TRYP 1 TRP CH2 ) 2.815576 2.815576 0.000000 16 Y ( TRYP 1 TRP CH2 ) -2.098381 -2.098381 0.000000 16 Z ( TRYP 1 TRP CH2 ) -1.487421 -1.487421 0.000000 17 X ( TRYP 1 TRP C ) 7.559132 7.559132 0.000000 17 Y ( TRYP 1 TRP C ) 35.133552 35.133552 0.000000 17 Z ( TRYP 1 TRP C ) 6.754142 6.754142 0.000000 18 X ( TRYP 1 TRP OT1 ) -7.217698 -7.217698 0.000000 18 Y ( TRYP 1 TRP OT1 ) -4.162769 -4.162769 0.000000 18 Z ( TRYP 1 TRP OT1 ) 13.234025 13.234025 0.000000 19 X ( TRYP 1 TRP OT2 ) -8.678905 -8.678905 0.000000 19 Y ( TRYP 1 TRP OT2 ) -4.792729 -4.792729 0.000000 19 Z ( TRYP 1 TRP OT2 ) -9.100835 -9.100835 0.000000 TESTFD: A total of 0 elements were within the tolerance X-PLOR> X-PLOR> X-PLOR>{* r-dielectric, switching *} X-PLOR>{* ======================= *} X-PLOR>parameter PARRDR> hbonds HBDSET> acceptor=true don=4.7 doff=5.2 dcut=5.7 aon=50.0 aoff=70.0 acut=90.0 HBDSET> end %HBDSET-ERR: inconsistent DCUT, TOLErance, DOFF given. Reset. PARRDR> nbonds NBDSET> atom rdie switch eps=1.0 NBDSET> cutnb=30.0 ctonnb=6.0 ctofnb=8.0 NBDSET> nbxmod=5 vswitch NBDSET> end PARRDR>end X-PLOR> X-PLOR> X-PLOR>test first selection= ( all ) step=0.000001 tol=0.0 end SELRPN: 19 atoms have been selected out of 19 MAKINB: mode 5 found 83 exclusions, 20 interactions(1-4) and 63 GB exclusions 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 TESTFD: Parameters: STEP= 0.00000 MASSweighting=F TESTFD: The following first derivatives differ by more than TOL= 0.000000 DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 1 X ( TRYP 1 TRP HT1 ) 0.949000 0.949000 0.000000 1 Y ( TRYP 1 TRP HT1 ) -5.693212 -5.693212 0.000000 1 Z ( TRYP 1 TRP HT1 ) -2.928266 -2.928266 0.000000 2 X ( TRYP 1 TRP HT2 ) 3.847620 3.847620 0.000000 2 Y ( TRYP 1 TRP HT2 ) -0.531003 -0.531003 0.000000 2 Z ( TRYP 1 TRP HT2 ) -1.638210 -1.638210 0.000000 3 X ( TRYP 1 TRP N ) -13.317048 -13.317048 0.000000 3 Y ( TRYP 1 TRP N ) -16.116270 -16.116270 0.000000 3 Z ( TRYP 1 TRP N ) -26.097968 -26.097968 0.000000 4 X ( TRYP 1 TRP HT3 ) 1.060898 1.060898 0.000000 4 Y ( TRYP 1 TRP HT3 ) -1.695066 -1.695066 0.000000 4 Z ( TRYP 1 TRP HT3 ) -0.695042 -0.695042 0.000000 5 X ( TRYP 1 TRP CA ) 15.906812 15.906812 0.000000 5 Y ( TRYP 1 TRP CA ) 7.040243 7.040243 0.000000 5 Z ( TRYP 1 TRP CA ) 25.597307 25.597307 0.000000 6 X ( TRYP 1 TRP CB ) -6.518070 -6.518070 0.000000 6 Y ( TRYP 1 TRP CB ) 5.476678 5.476678 0.000000 6 Z ( TRYP 1 TRP CB ) 2.995732 2.995732 0.000000 7 X ( TRYP 1 TRP CG ) -6.933872 -6.933872 0.000000 7 Y ( TRYP 1 TRP CG ) 1.675346 1.675346 0.000000 7 Z ( TRYP 1 TRP CG ) -14.397912 -14.397912 0.000000 8 X ( TRYP 1 TRP CD2 ) 31.295848 31.295848 0.000000 8 Y ( TRYP 1 TRP CD2 ) -22.156584 -22.156584 0.000000 8 Z ( TRYP 1 TRP CD2 ) 6.845789 6.845789 0.000000 9 X ( TRYP 1 TRP CE2 ) -25.045749 -25.045749 0.000000 9 Y ( TRYP 1 TRP CE2 ) 6.822352 6.822352 0.000000 9 Z ( TRYP 1 TRP CE2 ) 14.336628 14.336628 0.000000 10 X ( TRYP 1 TRP CE3 ) -16.448162 -16.448162 0.000000 10 Y ( TRYP 1 TRP CE3 ) 11.214020 11.214020 0.000000 10 Z ( TRYP 1 TRP CE3 ) 10.163320 10.163320 0.000000 11 X ( TRYP 1 TRP CD1 ) -4.857875 -4.857875 0.000000 11 Y ( TRYP 1 TRP CD1 ) -9.589924 -9.589924 0.000000 11 Z ( TRYP 1 TRP CD1 ) 1.654590 1.654590 0.000000 12 X ( TRYP 1 TRP NE1 ) 27.185189 27.185189 0.000000 12 Y ( TRYP 1 TRP NE1 ) 20.716238 20.716238 0.000000 12 Z ( TRYP 1 TRP NE1 ) -30.844470 -30.844470 0.000000 13 X ( TRYP 1 TRP HE1 ) -13.554457 -13.554457 0.000000 13 Y ( TRYP 1 TRP HE1 ) -10.404525 -10.404525 0.000000 13 Z ( TRYP 1 TRP HE1 ) -0.424350 -0.424350 0.000000 14 X ( TRYP 1 TRP CZ2 ) 9.166841 9.166841 0.000000 14 Y ( TRYP 1 TRP CZ2 ) -3.087236 -3.087236 0.000000 14 Z ( TRYP 1 TRP CZ2 ) 14.929255 14.929255 0.000000 15 X ( TRYP 1 TRP CZ3 ) -2.667623 -2.667623 0.000000 15 Y ( TRYP 1 TRP CZ3 ) 1.430240 1.430240 0.000000 15 Z ( TRYP 1 TRP CZ3 ) -2.070128 -2.070128 0.000000 16 X ( TRYP 1 TRP CH2 ) 2.815576 2.815576 0.000000 16 Y ( TRYP 1 TRP CH2 ) -2.098381 -2.098381 0.000000 16 Z ( TRYP 1 TRP CH2 ) -1.487421 -1.487421 0.000000 17 X ( TRYP 1 TRP C ) 7.188280 7.188280 0.000000 17 Y ( TRYP 1 TRP C ) 36.572235 36.572235 0.000000 17 Z ( TRYP 1 TRP C ) 7.985746 7.985746 0.000000 18 X ( TRYP 1 TRP OT1 ) -3.478144 -3.478144 0.000000 18 Y ( TRYP 1 TRP OT1 ) -10.392787 -10.392787 0.000000 18 Z ( TRYP 1 TRP OT1 ) 11.220223 11.220223 0.000000 19 X ( TRYP 1 TRP OT2 ) -6.595064 -6.595064 0.000000 19 Y ( TRYP 1 TRP OT2 ) -9.182363 -9.182363 0.000000 19 Z ( TRYP 1 TRP OT2 ) -15.144823 -15.144823 0.000000 TESTFD: A total of 0 elements were within the tolerance X-PLOR> X-PLOR>{* repel option *} X-PLOR>{* ============ *} X-PLOR>flags exclude * include vdw end X-PLOR> X-PLOR>parameter PARRDR> nbonds NBDSET> atom repel=0.9 rexponent=2 irexponent=2 rconst=110. NBDSET> end PARRDR>end X-PLOR> X-PLOR> X-PLOR>test first selection= ( all ) step=0.000001 tol=0.0 end SELRPN: 19 atoms have been selected out of 19 MAKINB: mode 5 found 83 exclusions, 20 interactions(1-4) and 63 GB exclusions TESTFD: Parameters: STEP= 0.00000 MASSweighting=F TESTFD: The following first derivatives differ by more than TOL= 0.000000 DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 1 X ( TRYP 1 TRP HT1 ) 49.869381 49.869381 0.000000 1 Y ( TRYP 1 TRP HT1 ) 429.638318 429.638318 0.000000 1 Z ( TRYP 1 TRP HT1 ) 473.002512 473.002512 0.000000 2 X ( TRYP 1 TRP HT2 ) 902.203887 902.203886 0.000000 2 Y ( TRYP 1 TRP HT2 ) 141.843732 141.843732 0.000000 2 Z ( TRYP 1 TRP HT2 ) -495.252354 -495.252354 0.000000 3 X ( TRYP 1 TRP N ) 302.689395 302.689395 0.000000 3 Y ( TRYP 1 TRP N ) 1448.376952 1448.376952 0.000000 3 Z ( TRYP 1 TRP N ) 397.068101 397.068100 0.000000 4 X ( TRYP 1 TRP HT3 ) 0.000000 0.000000 0.000000 4 Y ( TRYP 1 TRP HT3 ) 0.000000 0.000000 0.000000 4 Z ( TRYP 1 TRP HT3 ) 0.000000 0.000000 0.000000 5 X ( TRYP 1 TRP CA ) 1013.416749 1013.416749 0.000000 5 Y ( TRYP 1 TRP CA ) -159.684539 -159.684539 0.000000 5 Z ( TRYP 1 TRP CA ) -768.943384 -768.943384 0.000000 6 X ( TRYP 1 TRP CB ) 467.706705 467.706705 0.000000 6 Y ( TRYP 1 TRP CB ) -596.319391 -596.319390 0.000000 6 Z ( TRYP 1 TRP CB ) -1357.430652 -1357.430652 0.000000 7 X ( TRYP 1 TRP CG ) -1062.173153 -1062.173153 0.000000 7 Y ( TRYP 1 TRP CG ) -322.422497 -322.422497 0.000000 7 Z ( TRYP 1 TRP CG ) -156.961797 -156.961797 0.000000 8 X ( TRYP 1 TRP CD2 ) -86.474567 -86.474567 0.000000 8 Y ( TRYP 1 TRP CD2 ) -8.122814 -8.122814 0.000000 8 Z ( TRYP 1 TRP CD2 ) -0.466513 -0.466513 0.000000 9 X ( TRYP 1 TRP CE2 ) 0.000000 0.000000 0.000000 9 Y ( TRYP 1 TRP CE2 ) 0.000000 0.000000 0.000000 9 Z ( TRYP 1 TRP CE2 ) 0.000000 0.000000 0.000000 10 X ( TRYP 1 TRP CE3 ) -1912.473168 -1912.473168 0.000000 10 Y ( TRYP 1 TRP CE3 ) 575.399698 575.399698 0.000000 10 Z ( TRYP 1 TRP CE3 ) 2651.629921 2651.629921 0.000000 11 X ( TRYP 1 TRP CD1 ) -433.798577 -433.798577 0.000000 11 Y ( TRYP 1 TRP CD1 ) 54.132619 54.132618 0.000000 11 Z ( TRYP 1 TRP CD1 ) -34.142613 -34.142613 0.000000 12 X ( TRYP 1 TRP NE1 ) 0.000000 0.000000 0.000000 12 Y ( TRYP 1 TRP NE1 ) 0.000000 0.000000 0.000000 12 Z ( TRYP 1 TRP NE1 ) 0.000000 0.000000 0.000000 13 X ( TRYP 1 TRP HE1 ) 0.000000 0.000000 0.000000 13 Y ( TRYP 1 TRP HE1 ) 0.000000 0.000000 0.000000 13 Z ( TRYP 1 TRP HE1 ) 0.000000 0.000000 0.000000 14 X ( TRYP 1 TRP CZ2 ) 0.000000 0.000000 0.000000 14 Y ( TRYP 1 TRP CZ2 ) 0.000000 0.000000 0.000000 14 Z ( TRYP 1 TRP CZ2 ) 0.000000 0.000000 0.000000 15 X ( TRYP 1 TRP CZ3 ) 0.000000 0.000000 0.000000 15 Y ( TRYP 1 TRP CZ3 ) 0.000000 0.000000 0.000000 15 Z ( TRYP 1 TRP CZ3 ) 0.000000 0.000000 0.000000 16 X ( TRYP 1 TRP CH2 ) 0.000000 0.000000 0.000000 16 Y ( TRYP 1 TRP CH2 ) 0.000000 0.000000 0.000000 16 Z ( TRYP 1 TRP CH2 ) 0.000000 0.000000 0.000000 17 X ( TRYP 1 TRP C ) -49.869381 -49.869381 0.000000 17 Y ( TRYP 1 TRP C ) -429.638318 -429.638318 0.000000 17 Z ( TRYP 1 TRP C ) -473.002512 -473.002512 0.000000 18 X ( TRYP 1 TRP OT1 ) 808.902730 808.902730 0.000000 18 Y ( TRYP 1 TRP OT1 ) -1133.203760 -1133.203760 0.000000 18 Z ( TRYP 1 TRP OT1 ) -235.500709 -235.500709 0.000000 19 X ( TRYP 1 TRP OT2 ) 0.000000 0.000000 0.000000 19 Y ( TRYP 1 TRP OT2 ) 0.000000 0.000000 0.000000 19 Z ( TRYP 1 TRP OT2 ) 0.000000 0.000000 0.000000 TESTFD: A total of 0 elements were within the tolerance X-PLOR> X-PLOR>parameter PARRDR> nbonds NBDSET> atom repel=0.9 rexponent=4 irexponent=1 rconst=110. NBDSET> end PARRDR>end X-PLOR> X-PLOR> X-PLOR>test first selection= ( all ) step=0.000001 tol=0.0 end SELRPN: 19 atoms have been selected out of 19 MAKINB: mode 5 found 83 exclusions, 20 interactions(1-4) and 63 GB exclusions TESTFD: Parameters: STEP= 0.00000 MASSweighting=F TESTFD: The following first derivatives differ by more than TOL= 0.000000 DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 1 X ( TRYP 1 TRP HT1 ) 0.082876 0.082876 0.000000 1 Y ( TRYP 1 TRP HT1 ) 0.714001 0.714001 0.000000 1 Z ( TRYP 1 TRP HT1 ) 0.786067 0.786067 0.000000 2 X ( TRYP 1 TRP HT2 ) 2.127336 2.127336 0.000000 2 Y ( TRYP 1 TRP HT2 ) 0.348634 0.348634 0.000000 2 Z ( TRYP 1 TRP HT2 ) -1.291945 -1.291945 0.000000 3 X ( TRYP 1 TRP N ) -1.222548 -1.222548 0.000000 3 Y ( TRYP 1 TRP N ) 3.736551 3.736551 0.000000 3 Z ( TRYP 1 TRP N ) 0.886268 0.886268 0.000000 4 X ( TRYP 1 TRP HT3 ) 0.000000 0.000000 0.000000 4 Y ( TRYP 1 TRP HT3 ) 0.000000 0.000000 0.000000 4 Z ( TRYP 1 TRP HT3 ) 0.000000 0.000000 0.000000 5 X ( TRYP 1 TRP CA ) 0.131269 0.131269 0.000000 5 Y ( TRYP 1 TRP CA ) -0.021862 -0.021862 0.000000 5 Z ( TRYP 1 TRP CA ) -0.129682 -0.129682 0.000000 6 X ( TRYP 1 TRP CB ) 0.640235 0.640235 0.000000 6 Y ( TRYP 1 TRP CB ) -0.747342 -0.747342 0.000000 6 Z ( TRYP 1 TRP CB ) -1.675109 -1.675109 0.000000 7 X ( TRYP 1 TRP CG ) -1.077273 -1.077273 0.000000 7 Y ( TRYP 1 TRP CG ) -0.327006 -0.327006 0.000000 7 Z ( TRYP 1 TRP CG ) -0.159193 -0.159193 0.000000 8 X ( TRYP 1 TRP CD2 ) -0.001367 -0.001367 0.000000 8 Y ( TRYP 1 TRP CD2 ) -0.000128 -0.000128 0.000000 8 Z ( TRYP 1 TRP CD2 ) -0.000007 -0.000007 0.000000 9 X ( TRYP 1 TRP CE2 ) 0.000000 0.000000 0.000000 9 Y ( TRYP 1 TRP CE2 ) 0.000000 0.000000 0.000000 9 Z ( TRYP 1 TRP CE2 ) 0.000000 0.000000 0.000000 10 X ( TRYP 1 TRP CE3 ) -2.861909 -2.861909 0.000000 10 Y ( TRYP 1 TRP CE3 ) 0.416261 0.416261 0.000000 10 Z ( TRYP 1 TRP CE3 ) 3.099541 3.099541 0.000000 11 X ( TRYP 1 TRP CD1 ) -0.035647 -0.035647 0.000000 11 Y ( TRYP 1 TRP CD1 ) 0.004448 0.004448 0.000000 11 Z ( TRYP 1 TRP CD1 ) -0.002806 -0.002806 0.000000 12 X ( TRYP 1 TRP NE1 ) 0.000000 0.000000 0.000000 12 Y ( TRYP 1 TRP NE1 ) 0.000000 0.000000 0.000000 12 Z ( TRYP 1 TRP NE1 ) 0.000000 0.000000 0.000000 13 X ( TRYP 1 TRP HE1 ) 0.000000 0.000000 0.000000 13 Y ( TRYP 1 TRP HE1 ) 0.000000 0.000000 0.000000 13 Z ( TRYP 1 TRP HE1 ) 0.000000 0.000000 0.000000 14 X ( TRYP 1 TRP CZ2 ) 0.000000 0.000000 0.000000 14 Y ( TRYP 1 TRP CZ2 ) 0.000000 0.000000 0.000000 14 Z ( TRYP 1 TRP CZ2 ) 0.000000 0.000000 0.000000 15 X ( TRYP 1 TRP CZ3 ) 0.000000 0.000000 0.000000 15 Y ( TRYP 1 TRP CZ3 ) 0.000000 0.000000 0.000000 15 Z ( TRYP 1 TRP CZ3 ) 0.000000 0.000000 0.000000 16 X ( TRYP 1 TRP CH2 ) 0.000000 0.000000 0.000000 16 Y ( TRYP 1 TRP CH2 ) 0.000000 0.000000 0.000000 16 Z ( TRYP 1 TRP CH2 ) 0.000000 0.000000 0.000000 17 X ( TRYP 1 TRP C ) -0.082876 -0.082876 0.000000 17 Y ( TRYP 1 TRP C ) -0.714001 -0.714001 0.000000 17 Z ( TRYP 1 TRP C ) -0.786067 -0.786067 0.000000 18 X ( TRYP 1 TRP OT1 ) 2.299904 2.299904 0.000000 18 Y ( TRYP 1 TRP OT1 ) -3.409557 -3.409557 0.000000 18 Z ( TRYP 1 TRP OT1 ) -0.727067 -0.727067 0.000000 19 X ( TRYP 1 TRP OT2 ) 0.000000 0.000000 0.000000 19 Y ( TRYP 1 TRP OT2 ) 0.000000 0.000000 0.000000 19 Z ( TRYP 1 TRP OT2 ) 0.000000 0.000000 0.000000 TESTFD: A total of 0 elements were within the tolerance X-PLOR> X-PLOR>parameter PARRDR> nbonds NBDSET> atom repel=0.9 rexponent=2 irexponent=2 rconst=110. NBDSET> end PARRDR>end X-PLOR> X-PLOR> X-PLOR>test first selection= ( all ) step=0.000001 tol=0.0 end SELRPN: 19 atoms have been selected out of 19 MAKINB: mode 5 found 83 exclusions, 20 interactions(1-4) and 63 GB exclusions TESTFD: Parameters: STEP= 0.00000 MASSweighting=F TESTFD: The following first derivatives differ by more than TOL= 0.000000 DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 1 X ( TRYP 1 TRP HT1 ) 49.869381 49.869381 0.000000 1 Y ( TRYP 1 TRP HT1 ) 429.638318 429.638318 0.000000 1 Z ( TRYP 1 TRP HT1 ) 473.002512 473.002512 0.000000 2 X ( TRYP 1 TRP HT2 ) 902.203887 902.203886 0.000000 2 Y ( TRYP 1 TRP HT2 ) 141.843732 141.843732 0.000000 2 Z ( TRYP 1 TRP HT2 ) -495.252354 -495.252354 0.000000 3 X ( TRYP 1 TRP N ) 302.689395 302.689395 0.000000 3 Y ( TRYP 1 TRP N ) 1448.376952 1448.376952 0.000000 3 Z ( TRYP 1 TRP N ) 397.068101 397.068100 0.000000 4 X ( TRYP 1 TRP HT3 ) 0.000000 0.000000 0.000000 4 Y ( TRYP 1 TRP HT3 ) 0.000000 0.000000 0.000000 4 Z ( TRYP 1 TRP HT3 ) 0.000000 0.000000 0.000000 5 X ( TRYP 1 TRP CA ) 1013.416749 1013.416749 0.000000 5 Y ( TRYP 1 TRP CA ) -159.684539 -159.684539 0.000000 5 Z ( TRYP 1 TRP CA ) -768.943384 -768.943384 0.000000 6 X ( TRYP 1 TRP CB ) 467.706705 467.706705 0.000000 6 Y ( TRYP 1 TRP CB ) -596.319391 -596.319390 0.000000 6 Z ( TRYP 1 TRP CB ) -1357.430652 -1357.430652 0.000000 7 X ( TRYP 1 TRP CG ) -1062.173153 -1062.173153 0.000000 7 Y ( TRYP 1 TRP CG ) -322.422497 -322.422497 0.000000 7 Z ( TRYP 1 TRP CG ) -156.961797 -156.961797 0.000000 8 X ( TRYP 1 TRP CD2 ) -86.474567 -86.474567 0.000000 8 Y ( TRYP 1 TRP CD2 ) -8.122814 -8.122814 0.000000 8 Z ( TRYP 1 TRP CD2 ) -0.466513 -0.466513 0.000000 9 X ( TRYP 1 TRP CE2 ) 0.000000 0.000000 0.000000 9 Y ( TRYP 1 TRP CE2 ) 0.000000 0.000000 0.000000 9 Z ( TRYP 1 TRP CE2 ) 0.000000 0.000000 0.000000 10 X ( TRYP 1 TRP CE3 ) -1912.473168 -1912.473168 0.000000 10 Y ( TRYP 1 TRP CE3 ) 575.399698 575.399698 0.000000 10 Z ( TRYP 1 TRP CE3 ) 2651.629921 2651.629921 0.000000 11 X ( TRYP 1 TRP CD1 ) -433.798577 -433.798577 0.000000 11 Y ( TRYP 1 TRP CD1 ) 54.132619 54.132618 0.000000 11 Z ( TRYP 1 TRP CD1 ) -34.142613 -34.142613 0.000000 12 X ( TRYP 1 TRP NE1 ) 0.000000 0.000000 0.000000 12 Y ( TRYP 1 TRP NE1 ) 0.000000 0.000000 0.000000 12 Z ( TRYP 1 TRP NE1 ) 0.000000 0.000000 0.000000 13 X ( TRYP 1 TRP HE1 ) 0.000000 0.000000 0.000000 13 Y ( TRYP 1 TRP HE1 ) 0.000000 0.000000 0.000000 13 Z ( TRYP 1 TRP HE1 ) 0.000000 0.000000 0.000000 14 X ( TRYP 1 TRP CZ2 ) 0.000000 0.000000 0.000000 14 Y ( TRYP 1 TRP CZ2 ) 0.000000 0.000000 0.000000 14 Z ( TRYP 1 TRP CZ2 ) 0.000000 0.000000 0.000000 15 X ( TRYP 1 TRP CZ3 ) 0.000000 0.000000 0.000000 15 Y ( TRYP 1 TRP CZ3 ) 0.000000 0.000000 0.000000 15 Z ( TRYP 1 TRP CZ3 ) 0.000000 0.000000 0.000000 16 X ( TRYP 1 TRP CH2 ) 0.000000 0.000000 0.000000 16 Y ( TRYP 1 TRP CH2 ) 0.000000 0.000000 0.000000 16 Z ( TRYP 1 TRP CH2 ) 0.000000 0.000000 0.000000 17 X ( TRYP 1 TRP C ) -49.869381 -49.869381 0.000000 17 Y ( TRYP 1 TRP C ) -429.638318 -429.638318 0.000000 17 Z ( TRYP 1 TRP C ) -473.002512 -473.002512 0.000000 18 X ( TRYP 1 TRP OT1 ) 808.902730 808.902730 0.000000 18 Y ( TRYP 1 TRP OT1 ) -1133.203760 -1133.203760 0.000000 18 Z ( TRYP 1 TRP OT1 ) -235.500709 -235.500709 0.000000 19 X ( TRYP 1 TRP OT2 ) 0.000000 0.000000 0.000000 19 Y ( TRYP 1 TRP OT2 ) 0.000000 0.000000 0.000000 19 Z ( TRYP 1 TRP OT2 ) 0.000000 0.000000 0.000000 TESTFD: A total of 0 elements were within the tolerance X-PLOR> X-PLOR>parameter PARRDR> nbonds NBDSET> atom repel=0.9 rexponent=2 irexponent=1 rconst=110. NBDSET> end PARRDR>end X-PLOR> X-PLOR> X-PLOR>test first selection= ( all ) step=0.000001 tol=0.0 end SELRPN: 19 atoms have been selected out of 19 MAKINB: mode 5 found 83 exclusions, 20 interactions(1-4) and 63 GB exclusions TESTFD: Parameters: STEP= 0.00000 MASSweighting=F TESTFD: The following first derivatives differ by more than TOL= 0.000000 DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 1 X ( TRYP 1 TRP HT1 ) 2.298397 2.298397 0.000000 1 Y ( TRYP 1 TRP HT1 ) 19.801315 19.801315 0.000000 1 Z ( TRYP 1 TRP HT1 ) 21.799899 21.799899 0.000000 2 X ( TRYP 1 TRP HT2 ) 36.477429 36.477429 0.000000 2 Y ( TRYP 1 TRP HT2 ) 5.755661 5.755661 0.000000 2 Z ( TRYP 1 TRP HT2 ) -20.205188 -20.205188 0.000000 3 X ( TRYP 1 TRP N ) 2.953266 2.953266 0.000000 3 Y ( TRYP 1 TRP N ) 46.709977 46.709977 0.000000 3 Z ( TRYP 1 TRP N ) 12.336094 12.336094 0.000000 4 X ( TRYP 1 TRP HT3 ) 0.000000 0.000000 0.000000 4 Y ( TRYP 1 TRP HT3 ) 0.000000 0.000000 0.000000 4 Z ( TRYP 1 TRP HT3 ) 0.000000 0.000000 0.000000 5 X ( TRYP 1 TRP CA ) 18.670903 18.670903 0.000000 5 Y ( TRYP 1 TRP CA ) -2.858343 -2.858343 0.000000 5 Z ( TRYP 1 TRP CA ) -12.030150 -12.030150 0.000000 6 X ( TRYP 1 TRP CB ) 10.646898 10.646898 0.000000 6 Y ( TRYP 1 TRP CB ) -13.700740 -13.700740 0.000000 6 Z ( TRYP 1 TRP CB ) -31.235391 -31.235391 0.000000 7 X ( TRYP 1 TRP CG ) -28.603639 -28.603639 0.000000 7 Y ( TRYP 1 TRP CG ) -8.682630 -8.682630 0.000000 7 Z ( TRYP 1 TRP CG ) -4.226880 -4.226880 0.000000 8 X ( TRYP 1 TRP CD2 ) -3.200406 -3.200406 0.000000 8 Y ( TRYP 1 TRP CD2 ) -0.300624 -0.300624 0.000000 8 Z ( TRYP 1 TRP CD2 ) -0.017266 -0.017266 0.000000 9 X ( TRYP 1 TRP CE2 ) 0.000000 0.000000 0.000000 9 Y ( TRYP 1 TRP CE2 ) 0.000000 0.000000 0.000000 9 Z ( TRYP 1 TRP CE2 ) 0.000000 0.000000 0.000000 10 X ( TRYP 1 TRP CE3 ) -54.391978 -54.391978 0.000000 10 Y ( TRYP 1 TRP CE3 ) 10.107780 10.107780 0.000000 10 Z ( TRYP 1 TRP CE3 ) 64.115519 64.115519 0.000000 11 X ( TRYP 1 TRP CD1 ) -9.451390 -9.451390 0.000000 11 Y ( TRYP 1 TRP CD1 ) 1.179415 1.179415 0.000000 11 Z ( TRYP 1 TRP CD1 ) -0.743882 -0.743882 0.000000 12 X ( TRYP 1 TRP NE1 ) 0.000000 0.000000 0.000000 12 Y ( TRYP 1 TRP NE1 ) 0.000000 0.000000 0.000000 12 Z ( TRYP 1 TRP NE1 ) 0.000000 0.000000 0.000000 13 X ( TRYP 1 TRP HE1 ) 0.000000 0.000000 0.000000 13 Y ( TRYP 1 TRP HE1 ) 0.000000 0.000000 0.000000 13 Z ( TRYP 1 TRP HE1 ) 0.000000 0.000000 0.000000 14 X ( TRYP 1 TRP CZ2 ) 0.000000 0.000000 0.000000 14 Y ( TRYP 1 TRP CZ2 ) 0.000000 0.000000 0.000000 14 Z ( TRYP 1 TRP CZ2 ) 0.000000 0.000000 0.000000 15 X ( TRYP 1 TRP CZ3 ) 0.000000 0.000000 0.000000 15 Y ( TRYP 1 TRP CZ3 ) 0.000000 0.000000 0.000000 15 Z ( TRYP 1 TRP CZ3 ) 0.000000 0.000000 0.000000 16 X ( TRYP 1 TRP CH2 ) 0.000000 0.000000 0.000000 16 Y ( TRYP 1 TRP CH2 ) 0.000000 0.000000 0.000000 16 Z ( TRYP 1 TRP CH2 ) 0.000000 0.000000 0.000000 17 X ( TRYP 1 TRP C ) -2.298397 -2.298397 0.000000 17 Y ( TRYP 1 TRP C ) -19.801315 -19.801315 0.000000 17 Z ( TRYP 1 TRP C ) -21.799899 -21.799899 0.000000 18 X ( TRYP 1 TRP OT1 ) 26.898916 26.898916 0.000000 18 Y ( TRYP 1 TRP OT1 ) -38.210496 -38.210496 0.000000 18 Z ( TRYP 1 TRP OT1 ) -7.992856 -7.992856 0.000000 19 X ( TRYP 1 TRP OT2 ) 0.000000 0.000000 0.000000 19 Y ( TRYP 1 TRP OT2 ) 0.000000 0.000000 0.000000 19 Z ( TRYP 1 TRP OT2 ) 0.000000 0.000000 0.000000 TESTFD: A total of 0 elements were within the tolerance X-PLOR> X-PLOR>constraints interaction ( chemical O* ) ( chemical N* ) end SELRPN: 2 atoms have been selected out of 19 SELRPN: 2 atoms have been selected out of 19 X-PLOR> X-PLOR>vector do (x=4.) ( chemical O* ) SELRPN: 2 atoms have been selected out of 19 X-PLOR>vector do (y=4.) ( chemical O* ) SELRPN: 2 atoms have been selected out of 19 X-PLOR>vector do (z=4.) ( chemical O* ) SELRPN: 2 atoms have been selected out of 19 X-PLOR> X-PLOR>vector do (x=5.) ( chemical N* ) SELRPN: 2 atoms have been selected out of 19 X-PLOR>vector do (y=4.) ( chemical N* ) SELRPN: 2 atoms have been selected out of 19 X-PLOR>vector do (z=4.) ( chemical N* ) SELRPN: 2 atoms have been selected out of 19 X-PLOR> X-PLOR>parameter PARRDR> nbonds NBDSET> NBDSET> atom repel=0.89 rexponent=2 irexponent=1 rconst=110. cutnb=20. NBDSET> end PARRDR>end X-PLOR> X-PLOR> X-PLOR>parameter PARRDR> NONBONDED ( chemical O* ) 0.6469 2.8509 0.6469 2.8509 SELRPN: 2 atoms have been selected out of 19 PARRDR> nonbonded ( chemical N* ) 0.2384 2.8509 0.2384 2.8509 SELRPN: 2 atoms have been selected out of 19 PARRDR>end X-PLOR>energy end MAKINB: mode 5 found 2 exclusions, 2 interactions(1-4) and 0 GB exclusions %atoms "TRYP-1 -TRP -NE1 " and "TRYP-1 -TRP -OT1 " only 1.00 A apart %atoms "TRYP-1 -TRP -NE1 " and "TRYP-1 -TRP -OT2 " only 1.00 A apart --------------- cycle= 1 -------------------------------------------------- | Etotal =1502.685 grad(E)=215.404 E(VDW )=1502.685 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>parameter PARRDR> nbfix ( chemical O* ) ( chemical N* ) 1000000. 10. 1000000. 10. SELRPN: 2 atoms have been selected out of 19 SELRPN: 2 atoms have been selected out of 19 PARRDR>end X-PLOR>energy end --------------- cycle= 2 -------------------------------------------------- | Etotal =6540.177 grad(E)=289.315 E(VDW )=6540.177 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>vector do ( chemical=N) ( chemical N* ) Assuming literal string "N" SELRPN: 2 atoms have been selected out of 19 X-PLOR>vector do (chemical=O) ( chemical O* ) Assuming literal string "O" SELRPN: 2 atoms have been selected out of 19 X-PLOR> X-PLOR>delete selection=( not (chemical O or chemical N ) ) end SELRPN: 15 atoms have been selected out of 19 MAPIC: Atom numbers being modified SCRATC-warning: CONStraints INTEraction selections erased. XPLOR: current counts (number in parenthesis is maximum) NATOM= 4(MAXA= 200) NBOND= 0(MAXB= 100) NTHETA= 0(MAXT= 100) NGRP= 3(MAXGRP= 100) NPHI= 0(MAXP= 100) NIMPHI= 0(MAXIMP= 100) NDON= 0(MAXPAD= 100) NACC= 0(MAXPAD= 100) NNB= 0(MAXNB= 100) X-PLOR>constraints interaction ( chemical O* ) ( chemical N* ) end SELRPN: 2 atoms have been selected out of 4 SELRPN: 2 atoms have been selected out of 4 X-PLOR> X-PLOR>parameter PARRDR> reset PARRDR> NONBONDED O 0.6469 2.8509 0.6469 2.8509 PARRDR> nonbonded N 0.2384 2.8509 0.2384 2.8509 PARRDR>end X-PLOR> X-PLOR>energy end MAKINB: mode 5 found 0 exclusions, 0 interactions(1-4) and 0 GB exclusions %atoms "TRYP-1 -TRP -N " and "TRYP-1 -TRP -OT1 " only 1.00 A apart %atoms "TRYP-1 -TRP -N " and "TRYP-1 -TRP -OT2 " only 1.00 A apart %atoms "TRYP-1 -TRP -NE1 " and "TRYP-1 -TRP -OT1 " only 1.00 A apart %atoms "TRYP-1 -TRP -NE1 " and "TRYP-1 -TRP -OT2 " only 1.00 A apart --------------- cycle= 3 -------------------------------------------------- | Etotal =1502.685 grad(E)=469.461 E(VDW )=1502.685 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>parameter PARRDR> nbfix O N 1000000. 10. 1000000. 10. PARRDR>end X-PLOR> X-PLOR>energy end --------------- cycle= 4 -------------------------------------------------- | Etotal =10539.563 grad(E)=650.327 E(VDW )=10539.563 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR> X-PLOR>stop HEAP: maximum use= 631551 current use= 605745 X-PLOR: total CPU time= 0.0500 s X-PLOR: entry time at 15:33:20 11-Jun-07 X-PLOR: exit time at 15:33:20 11-Jun-07