XPLOR-NIH version 2.10-pre1 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: 09-Mar-05 12:09:57 X-PLOR>remarks param4.inp X-PLOR>remarks more tests for the atom and type-based parameters X-PLOR>remarks Axel T. Brunger X-PLOR>remarks ================================== X-PLOR> X-PLOR>topology reset @TOPPAR:topallhdg.pro end {* this is the DG-version of this file *} ASSFIL: file /home/schwitrs/xplor/toppar/topallhdg.pro opened. RTFRDR>remark file topallhdg.pro RTFRDR>remark geometric energy function topology for distance geometry and RTFRDR>remark simulated annealing. RTFRDR>remark RTFRDR>remark history: RTFRDR>remark RTFRDR>remark XPLOR topology file TOPALLHSA.PRO, all hydrogens, RTFRDR>remark for simulated annealing, to be used with PARALLHSA.PRO RTFRDR>remark based on TOPALLH6.PRO. RTFRDR>remark internal coordinates from TOPH19.PRO. RTFRDR> RTFRDR>! all dihedrals defining planarity have been converted to impropers, RTFRDR>! the only dihedrals left are around rotatable bonds. RTFRDR>! some additional impropers were included in the rings to define planarity RTFRDR>! better. patches are included to define chirality at stereospecifically RTFRDR>! assigned prochiral centres and convert from trans to cis peptide bond. RTFRDR>! modifications by M. Nilges and P. Kraulis. RTFRDR>! added stereospecific impropers for all pro-chiral centers (ATB) RTFRDR> RTFRDR> RTFRDR>set message off echo off end RTFRDR> end {* this is the DG-version of this file *} X-PLOR> X-PLOR>segment SEGMENT> name="TRYP" SEGMENT> chain CHAIN> LINK PEPP HEAD - * TAIL + PRO END { LINK to PRO } CHAIN> LINK PEPT HEAD - * TAIL + * END CHAIN> FIRSt PROP TAIL + PRO END { nter for PRO } CHAIN> FIRSt NTER TAIL + * END CHAIN> LAST CTER HEAD - * END CHAIN> 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= 27(MAXA= 200) NBOND= 28(MAXB= 100) NTHETA= 48(MAXT= 100) NGRP= 3(MAXGRP= 100) NPHI= 2(MAXP= 100) NIMPHI= 23(MAXIMP= 100) NDON= 0(MAXPAD= 0) NACC= 0(MAXPAD= 0) NNB= 6(MAXNB= 100) X-PLOR> X-PLOR>parameter PARRDR> @TOPPAR:parallhdg.pro ASSFIL: file /home/schwitrs/xplor/toppar/parallhdg.pro opened. PARRDR>remark file parallhdg.pro PARRDR>remark NOTE: these parameters are DEPRECATED. Please instead use protein.par. PARRDR>remark geometric energy function parameters for distance geometry and PARRDR>remark simulated annealing. PARRDR> PARRDR>set message off echo off end PARRDR> nbonds repel = 0.8 end PARRDR>end X-PLOR> X-PLOR>coor COOR>ATOM 1 CA TRP 1 1.331 1.246 0.096 1.00 0.00 TRYP COOR>ATOM 2 HA TRP 1 1.571 0.780 1.039 1.00 0.00 TRYP X-PLOR> X-PLOR>energy end MAKINB: mode 5 found 138 exclusions, 59 interactions(1-4) and 79 GB exclusions --------------- cycle= 1 -------------------------------------------------- | Etotal =5755.541 grad(E)=385.853 E(BOND)=6.740 E(ANGL)=14.591 | | E(DIHE)=0.000 E(IMPR)=5734.027 E(VDW )=0.184 E(ELEC)=0.000 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR> X-PLOR>parameter PARRDR> reset PARRDR> learn initialize selection=( all ) mode=nostatistics end SELRPN: 27 atoms have been selected out of 27 PARRDR> learn accumulate end PARRDR> learn terminate end PARRDR> bonds ( all ) ( all ) 500. TOKEN SELRPN: 27 atoms have been selected out of 27 SELRPN: 27 atoms have been selected out of 27 PARRDR> angles ( all ) ( all ) ( all ) 200. TOKEN SELRPN: 27 atoms have been selected out of 27 SELRPN: 27 atoms have been selected out of 27 SELRPN: 27 atoms have been selected out of 27 PARRDR> impropers ( all ) ( all ) ( all ) ( all ) 400. 0 TOKEN SELRPN: 27 atoms have been selected out of 27 SELRPN: 27 atoms have been selected out of 27 SELRPN: 27 atoms have been selected out of 27 SELRPN: 27 atoms have been selected out of 27 PARRDR> dihedrals ( all ) ( all ) ( all ) ( all ) 400. 0 TOKEN SELRPN: 27 atoms have been selected out of 27 SELRPN: 27 atoms have been selected out of 27 SELRPN: 27 atoms have been selected out of 27 SELRPN: 27 atoms have been selected out of 27 PARRDR> nonbonded ( all ) 0.1 1.0 0.1 1.0 SELRPN: 27 atoms have been selected out of 27 PARRDR> ? PARRDR>end X-PLOR> X-PLOR>energy end --------------- cycle= 2 -------------------------------------------------- | Etotal =0.000 grad(E)=0.000 E(BOND)=0.000 E(ANGL)=0.000 | | E(DIHE)=0.000 E(IMPR)=0.000 E(VDW )=0.000 E(ELEC)=0.000 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>parameter PARRDR> reset type PARRDR> reduce mode=statistics selection=( all ) end SELRPN: 27 atoms have been selected out of 27 REDUCE: creating 18 new bond parameters REDUCE: creating 34 new angle parameters REDUCE: creating 2 new dihedral parameters REDUCE: creating 20 new improper parameters PARRDR> ? BOND C CT 999999.000 {sd= 0.001} 1.531 BOND C OC 758714.150 {sd= 0.001} 1.220 BOND CA CA 13795.151 {sd= 0.005} 1.397 BOND CA CB 999999.000 {sd= 0.001} 1.426 BOND CA CN 999999.000 {sd= 0.001} 1.395 BOND CA HA 120619.214 {sd= 0.002} 1.080 BOND CB CN 999999.000 {sd= 0.001} 1.422 BOND CB CX 999999.000 {sd= 0.001} 1.497 BOND CN NA 999999.000 {sd= 0.001} 1.373 BOND CT CT 999999.000 {sd= 0.001} 1.555 BOND CT CX 999999.000 {sd= 0.001} 1.551 BOND CT HA 21951.183 {sd= 0.004} 1.078 BOND CT NH3 999999.000 {sd= 0.001} 1.492 BOND CW CX 999999.000 {sd= 0.001} 1.379 BOND CW HA 999999.000 {sd= 0.001} 1.083 BOND CW NA 999999.000 {sd= 0.001} 1.377 BOND H NA 999999.000 {sd= 0.001} 0.980 BOND HC NH3 540180.945 {sd= 0.001} 1.040 ANGLe C CT CT 999999.00 {sd= 0.031} 108.6104 ANGLe C CT HA 999999.00 {sd= 0.031} 108.6131 ANGLe C CT NH3 999999.00 {sd= 0.031} 108.4762 ANGLe CA CA CA 9546.97 {sd= 0.319} 120.2719 ANGLe CA CA CB 999999.00 {sd= 0.031} 120.7614 ANGLe CA CA CN 999999.00 {sd= 0.031} 119.9172 ANGLe CA CA HA 4724.85 {sd= 0.454} 119.7045 ANGLe CA CB CN 999999.00 {sd= 0.031} 116.7580 ANGLe CA CB CX 999999.00 {sd= 0.031} 135.0761 ANGLe CA CN CB 999999.00 {sd= 0.031} 122.0193 ANGLe CA CN NA 999999.00 {sd= 0.031} 132.8143 ANGLe CB CA HA 999999.00 {sd= 0.031} 120.4957 ANGLe CB CN NA 999999.00 {sd= 0.031} 105.1664 ANGLe CB CX CT 999999.00 {sd= 0.031} 130.4199 ANGLe CB CX CW 999999.00 {sd= 0.031} 104.5826 ANGLe CN CA HA 999999.00 {sd= 0.031} 120.0541 ANGLe CN CB CX 999999.00 {sd= 0.031} 108.1640 ANGLe CN NA CW 999999.00 {sd= 0.031} 112.5925 ANGLe CN NA H 999999.00 {sd= 0.031} 122.6125 ANGLe CT C OC ********* {sd= 0.002} 117.9845 ANGLe CT CT CX 999999.00 {sd= 0.031} 112.9045 ANGLe CT CT HA 930.42 {sd= 1.022} 109.0317 ANGLe CT CT NH3 999999.00 {sd= 0.031} 111.0932 ANGLe CT CX CW 999999.00 {sd= 0.031} 124.9744 ANGLe CT NH3 HC 121546.78 {sd= 0.089} 109.5192 ANGLe CW NA H 999999.00 {sd= 0.031} 124.7944 ANGLe CX CT HA 8779.86 {sd= 0.333} 110.0084 ANGLe CX CW HA 999999.00 {sd= 0.031} 126.3190 ANGLe CX CW NA 999999.00 {sd= 0.031} 109.4866 ANGLe HA CT HA 999999.00 {sd= 0.031} 107.1046 ANGLe HA CT NH3 999999.00 {sd= 0.031} 109.5132 ANGLe HA CW NA 999999.00 {sd= 0.031} 124.1813 ANGLe HC NH3 HC 123759.13 {sd= 0.089} 109.4232 ANGLe OC C OC 999999.00 {sd= 0.031} 124.0310 DIHEdral CT CT CX CW 999999.00 {sd= 0.031} 0 -83.5693 DIHEdral CX CT CT NH3 999999.00 {sd= 0.031} 0 -60.4911 IMPRoper C CT OC OC 999999.00 {sd= 0.031} 0 0.0179 IMPRoper CA CA CA CA 999999.00 {sd= 0.031} 0 0.1281 IMPRoper CA CA CA CB 999999.00 {sd= 0.031} 0 0.0131 IMPRoper CA CA CA CN 999999.00 {sd= 0.031} 0 -0.1287 IMPRoper CA CA CA HA 67979.17 {sd= 0.120} 0 180.0336 IMPRoper CA CA CB CN 999999.00 {sd= 0.031} 0 -0.1461 IMPRoper CA CA CB CX 999999.00 {sd= 0.031} 0 -179.5680 IMPRoper CA CA CN CB 999999.00 {sd= 0.031} 0 -0.0118 IMPRoper CA CA CN NA 999999.00 {sd= 0.031} 0 179.9821 IMPRoper CA CB CN CA 999999.00 {sd= 0.031} 0 0.1466 IMPRoper CA CB CN NA 999999.00 {sd= 0.031} 0 -179.8488 IMPRoper CA CB CX CW 999999.00 {sd= 0.031} 0 -179.8095 IMPRoper CA CN CB CX 999999.00 {sd= 0.031} 0 179.7170 IMPRoper CA CN NA CW 999999.00 {sd= 0.031} 0 179.7098 IMPRoper CB CN NA H 999999.00 {sd= 0.031} 0 179.9734 IMPRoper CN CB CX CT 999999.00 {sd= 0.031} 0 179.0161 IMPRoper CN NA CW HA 999999.00 {sd= 0.031} 0 179.5564 IMPRoper CT C NH3 HA 999999.00 {sd= 0.031} 0 66.3444 IMPRoper CX CT HA HA 999999.00 {sd= 0.031} 0 71.1140 IMPRoper HC CT HC HC 999999.00 {sd= 0.031} 0 66.2307 PARRDR>end X-PLOR> X-PLOR>vector do (segid=chemical) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (chemical="C" ) ( name C* ) SELRPN: 11 atoms have been selected out of 27 X-PLOR>vector do (chemical="N" ) ( name N* ) SELRPN: 2 atoms have been selected out of 27 X-PLOR>vector do (chemical="O" ) ( name O* ) SELRPN: 2 atoms have been selected out of 27 X-PLOR>vector do (chemical="H" ) ( name H* ) SELRPN: 12 atoms have been selected out of 27 X-PLOR> X-PLOR>parameter PARRDR> reset type PARRDR> reduce mode=statistics selection=( all ) end SELRPN: 27 atoms have been selected out of 27 REDUCE: creating 5 new bond parameters REDUCE: creating 10 new angle parameters REDUCE: creating 2 new dihedral parameters REDUCE: creating 9 new improper parameters PARRDR>end X-PLOR> X-PLOR>write parameter output=OUTPUT end BOND C C 68.400 {sd= 0.066} 1.450 BOND C H 32619.905 {sd= 0.003} 1.079 BOND C N 96.678 {sd= 0.055} 1.414 BOND C O 758714.150 {sd= 0.001} 1.220 BOND H N 438.836 {sd= 0.026} 1.025 ANGLe C C C 13.79 {sd= 8.394} 118.8255 ANGLe C C H 29.04 {sd= 5.785} 116.0547 ANGLe C C N 9.93 {sd= 9.895} 113.4073 ANGLe C C O ********* {sd= 0.002} 117.9845 ANGLe C N C 999999.00 {sd= 0.031} 112.5925 ANGLe C N H 19.93 {sd= 6.983} 115.1929 ANGLe H C H 999999.00 {sd= 0.031} 107.1046 ANGLe H C N 18.07 {sd= 7.334} 116.8473 ANGLe H N H 123759.13 {sd= 0.089} 109.4232 ANGLe O C O 999999.00 {sd= 0.031} 124.0310 DIHEdral C C C C 999999.00 {sd= 0.031} 0 -83.5693 DIHEdral C C C N 999999.00 {sd= 0.031} 0 -60.4911 IMPRoper C C C C 0.12 {sd= 88.261} 0 -72.0643 IMPRoper C C C H 67979.17 {sd= 0.120} 0 180.0336 IMPRoper C C C N 136002.58 {sd= 0.085} 0 180.0667 IMPRoper C C H H 999999.00 {sd= 0.031} 0 71.1140 IMPRoper C C N C 999999.00 {sd= 0.031} 0 179.7098 IMPRoper C C N H 0.30 {sd= 56.815} 0 123.1589 IMPRoper C C O O 999999.00 {sd= 0.031} 0 0.0179 IMPRoper C N C H 999999.00 {sd= 0.031} 0 179.5564 IMPRoper H C H H 999999.00 {sd= 0.031} 0 66.2307 X-PLOR> X-PLOR>vector do (chemical=segid) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do ( segid=" " ) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR> X-PLOR>parameter PARRDR> reset type PARRDR> reduce mode=average selection=( all ) end SELRPN: 27 atoms have been selected out of 27 REDUCE: creating 18 new bond parameters REDUCE: creating 34 new angle parameters REDUCE: creating 2 new dihedral parameters REDUCE: creating 20 new improper parameters PARRDR> reset atom PARRDR> nonbonded ( all ) 0.1 1.0 0.1 1.0 SELRPN: 27 atoms have been selected out of 27 PARRDR> ? BOND C CT 500.000 {sd= 0.024} 1.531 BOND C OC 500.000 {sd= 0.024} 1.220 BOND CA CA 500.000 {sd= 0.024} 1.397 BOND CA CB 500.000 {sd= 0.024} 1.426 BOND CA CN 500.000 {sd= 0.024} 1.395 BOND CA HA 500.000 {sd= 0.024} 1.080 BOND CB CN 500.000 {sd= 0.024} 1.422 BOND CB CX 500.000 {sd= 0.024} 1.497 BOND CN NA 500.000 {sd= 0.024} 1.373 BOND CT CT 500.000 {sd= 0.024} 1.555 BOND CT CX 500.000 {sd= 0.024} 1.551 BOND CT HA 500.000 {sd= 0.024} 1.078 BOND CT NH3 500.000 {sd= 0.024} 1.492 BOND CW CX 500.000 {sd= 0.024} 1.379 BOND CW HA 500.000 {sd= 0.024} 1.083 BOND CW NA 500.000 {sd= 0.024} 1.377 BOND H NA 500.000 {sd= 0.024} 0.980 BOND HC NH3 500.000 {sd= 0.024} 1.040 ANGLe C CT CT 200.00 {sd= 2.205} 108.6104 ANGLe C CT HA 200.00 {sd= 2.205} 108.6131 ANGLe C CT NH3 200.00 {sd= 2.205} 108.4762 ANGLe CA CA CA 200.00 {sd= 2.205} 120.2719 ANGLe CA CA CB 200.00 {sd= 2.205} 120.7614 ANGLe CA CA CN 200.00 {sd= 2.205} 119.9172 ANGLe CA CA HA 200.00 {sd= 2.205} 119.7045 ANGLe CA CB CN 200.00 {sd= 2.205} 116.7580 ANGLe CA CB CX 200.00 {sd= 2.205} 135.0761 ANGLe CA CN CB 200.00 {sd= 2.205} 122.0193 ANGLe CA CN NA 200.00 {sd= 2.205} 132.8143 ANGLe CB CA HA 200.00 {sd= 2.205} 120.4957 ANGLe CB CN NA 200.00 {sd= 2.205} 105.1664 ANGLe CB CX CT 200.00 {sd= 2.205} 130.4199 ANGLe CB CX CW 200.00 {sd= 2.205} 104.5826 ANGLe CN CA HA 200.00 {sd= 2.205} 120.0541 ANGLe CN CB CX 200.00 {sd= 2.205} 108.1640 ANGLe CN NA CW 200.00 {sd= 2.205} 112.5925 ANGLe CN NA H 200.00 {sd= 2.205} 122.6125 ANGLe CT C OC 200.00 {sd= 2.205} 117.9845 ANGLe CT CT CX 200.00 {sd= 2.205} 112.9045 ANGLe CT CT HA 200.00 {sd= 2.205} 109.0317 ANGLe CT CT NH3 200.00 {sd= 2.205} 111.0932 ANGLe CT CX CW 200.00 {sd= 2.205} 124.9744 ANGLe CT NH3 HC 200.00 {sd= 2.205} 109.5192 ANGLe CW NA H 200.00 {sd= 2.205} 124.7944 ANGLe CX CT HA 200.00 {sd= 2.205} 110.0084 ANGLe CX CW HA 200.00 {sd= 2.205} 126.3190 ANGLe CX CW NA 200.00 {sd= 2.205} 109.4866 ANGLe HA CT HA 200.00 {sd= 2.205} 107.1046 ANGLe HA CT NH3 200.00 {sd= 2.205} 109.5132 ANGLe HA CW NA 200.00 {sd= 2.205} 124.1813 ANGLe HC NH3 HC 200.00 {sd= 2.205} 109.4232 ANGLe OC C OC 200.00 {sd= 2.205} 124.0310 DIHEdral CT CT CX CW 400.00 {sd= 1.559} 0 -83.5693 DIHEdral CX CT CT NH3 400.00 {sd= 1.559} 0 -60.4911 IMPRoper C CT OC OC 400.00 {sd= 1.559} 0 0.0179 IMPRoper CA CA CA CA 400.00 {sd= 1.559} 0 0.1281 IMPRoper CA CA CA CB 400.00 {sd= 1.559} 0 0.0131 IMPRoper CA CA CA CN 400.00 {sd= 1.559} 0 -0.1287 IMPRoper CA CA CA HA 400.00 {sd= 1.559} 0 180.0336 IMPRoper CA CA CB CN 400.00 {sd= 1.559} 0 -0.1461 IMPRoper CA CA CB CX 400.00 {sd= 1.559} 0 -179.5680 IMPRoper CA CA CN CB 400.00 {sd= 1.559} 0 -0.0118 IMPRoper CA CA CN NA 400.00 {sd= 1.559} 0 179.9821 IMPRoper CA CB CN CA 400.00 {sd= 1.559} 0 0.1466 IMPRoper CA CB CN NA 400.00 {sd= 1.559} 0 -179.8488 IMPRoper CA CB CX CW 400.00 {sd= 1.559} 0 -179.8095 IMPRoper CA CN CB CX 400.00 {sd= 1.559} 0 179.7170 IMPRoper CA CN NA CW 400.00 {sd= 1.559} 0 179.7098 IMPRoper CB CN NA H 400.00 {sd= 1.559} 0 179.9734 IMPRoper CN CB CX CT 400.00 {sd= 1.559} 0 179.0161 IMPRoper CN NA CW HA 400.00 {sd= 1.559} 0 179.5564 IMPRoper CT C NH3 HA 400.00 {sd= 1.559} 0 66.3444 IMPRoper CX CT HA HA 400.00 {sd= 1.559} 0 71.1140 IMPRoper HC CT HC HC 400.00 {sd= 1.559} 0 66.2307 PARRDR>end X-PLOR> X-PLOR>energy end --------------- cycle= 3 -------------------------------------------------- | Etotal =0.360 grad(E)=3.623 E(BOND)=0.059 E(ANGL)=0.295 | | E(DIHE)=0.000 E(IMPR)=0.007 E(VDW )=0.000 E(ELEC)=0.000 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>parameter PARRDR> reset PARRDR> ? PARRDR> reset all PARRDR> ? PARRDR>end X-PLOR> X-PLOR>stop HEAP: maximum use= 1138778 current use= 1107807 X-PLOR: total CPU time= 0.1800 s X-PLOR: entry time at 12:09:57 09-Mar-05 X-PLOR: exit time at 12:09:57 09-Mar-05