XPLOR-NIH version 2.15.1 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: schwitrs on: linen (x86/Linux ) at: 7-Sep-06 17:23:34 X-PLOR>remarks dgtest3.inp X-PLOR>remarks test metric matrix distrance geometry module -- X-PLOR>remarks basic tests on four connected atoms X-PLOR>remarks John Kuszewski and 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>flags FLAGS> include noe cdihe FLAGS>end X-PLOR> X-PLOR>{* delete everything except one dihedral angle *} X-PLOR>delete selection=( not ( name ca or name cb or name cg or name cd1 ) ) end SELRPN: 23 atoms have been selected out of 27 MAPIC: Atom numbers being modified XPLOR: current counts (number in parenthesis is maximum) NATOM= 4(MAXA= 200) NBOND= 3(MAXB= 100) NTHETA= 2(MAXT= 100) NGRP= 1(MAXGRP= 100) NPHI= 1(MAXP= 100) NIMPHI= 0(MAXIMP= 100) NDON= 0(MAXPAD= 0) NACC= 0(MAXPAD= 0) NNB= 0(MAXNB= 100) X-PLOR> X-PLOR>{* =============================================================== *} X-PLOR>{* test 1: test dihedral angle restraints *} X-PLOR>{* =============================================================== *} X-PLOR> X-PLOR> X-PLOR>constraints CONS> dihedral Obsolete syntax: please use REStraints DIHEdral DIHEDRAL> nassign=10 %CSTRAN: allocating space for 10 assignments. DIHEDRAL> assign ( name ca ) ( name cb ) ( name cg ) ( name cd1 ) 1. 70. 0.01 2 SELRPN: 1 atoms have been selected out of 4 SELRPN: 1 atoms have been selected out of 4 SELRPN: 1 atoms have been selected out of 4 SELRPN: 1 atoms have been selected out of 4 DIHEDRAL> end CONS>end X-PLOR> X-PLOR>flags include cdih end X-PLOR> X-PLOR>set seed=12345 end X-PLOR> X-PLOR>mmdg MMDG> verbose off MMDG> iacc=0.01 tacc=0.01 bacc=0.001 pacc=0.01 MMDG> random MMDG> metrize (all) 100 SELRPN: 4 atoms have been selected out of 4 MMDG>end MMDG: 4 atoms will be randomly metrized. DGSETNX: found 10 exclusions (1--2, 1--3) for repulsive lower bounds. X-PLOR> X-PLOR> X-PLOR>pick dihedral ( name ca ) ( name cb ) ( name cg ) ( name cd1 ) geometry SELRPN: 1 atoms have been selected out of 4 SELRPN: 1 atoms have been selected out of 4 SELRPN: 1 atoms have been selected out of 4 SELRPN: 1 atoms have been selected out of 4 GEOM= 69.353707 X-PLOR>print angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. (TRYP 1 CA |TRYP 1 CB |TRYP 1 CG ) 109.558 109.500 0.058 0.001 500.000 (TRYP 1 CB |TRYP 1 CG |TRYP 1 CD1 ) 124.767 125.000 -0.233 0.008 500.000 RMS deviation= 0.170 X-PLOR>print bonds (atom-i |atom-j ) dist. equil. delta energy const. (TRYP 1 CA |TRYP 1 CB ) 1.530 1.530 0.000 0.000 1000.000 (TRYP 1 CB |TRYP 1 CG ) 1.496 1.495 0.001 0.000 1000.000 (TRYP 1 CG |TRYP 1 CD1 ) 1.353 1.352 0.001 0.000 1000.000 RMS deviation= 0.000 X-PLOR> X-PLOR>{* =============================================================== *} X-PLOR>{* test 2: test inconsistency handling *} X-PLOR>{* =============================================================== *} X-PLOR> X-PLOR>constraints CONS> dihedral Obsolete syntax: please use REStraints DIHEdral DIHEDRAL> nassign=10 DIHEDRAL> assign ( name ca ) ( name cb ) ( name cg ) ( name cd1 ) 1. 70. 0.01 2 SELRPN: 1 atoms have been selected out of 4 SELRPN: 1 atoms have been selected out of 4 SELRPN: 1 atoms have been selected out of 4 SELRPN: 1 atoms have been selected out of 4 DIHEDRAL> assign ( name ca ) ( name cb ) ( name cg ) ( name cd1 ) 1. 80. 0.01 2 SELRPN: 1 atoms have been selected out of 4 SELRPN: 1 atoms have been selected out of 4 SELRPN: 1 atoms have been selected out of 4 SELRPN: 1 atoms have been selected out of 4 DIHEDRAL> end CONS>end X-PLOR> X-PLOR>set seed=12345 end X-PLOR> X-PLOR>mmdg MMDG> verbose off MMDG> iacc=0.01 tacc=0.01 bacc=0.001 pacc=0.01 MMDG> random MMDG> metrize (all) 100 SELRPN: 4 atoms have been selected out of 4 MMDG>end MMDG: 4 atoms will be randomly metrized. DGSETNX: found 10 exclusions (1--2, 1--3) for repulsive lower bounds. TRYP 1 CD1 TRYP 1 CA 3.1611 3.1619 3.2323 * * Geometric inconsistency--lower bound greater than upper. Attempted to continue by inverting these bounds. %DISGEO-ERR: There are geometric inconsistencies. Proceed at own risk. X-PLOR> X-PLOR> X-PLOR>pick dihedral ( name ca ) ( name cb ) ( name cg ) ( name cd1 ) geometry SELRPN: 1 atoms have been selected out of 4 SELRPN: 1 atoms have been selected out of 4 SELRPN: 1 atoms have been selected out of 4 SELRPN: 1 atoms have been selected out of 4 GEOM= 71.074226 X-PLOR> X-PLOR>{* =============================================================== *} X-PLOR>{* test 3: test flags (turning on/off of terms) *} X-PLOR>{* =============================================================== *} X-PLOR>flags exclude cdihe end X-PLOR> X-PLOR>set seed=12345 end X-PLOR> X-PLOR>mmdg MMDG> verbose off MMDG> iacc=0.01 tacc=0.01 bacc=0.001 pacc=0.01 MMDG> random MMDG> metrize (all) 100 SELRPN: 4 atoms have been selected out of 4 MMDG>end MMDG: 4 atoms will be randomly metrized. DGSETNX: found 10 exclusions (1--2, 1--3) for repulsive lower bounds. X-PLOR> X-PLOR>pick dihedral ( name ca ) ( name cb ) ( name cg ) ( name cd1 ) geometry SELRPN: 1 atoms have been selected out of 4 SELRPN: 1 atoms have been selected out of 4 SELRPN: 1 atoms have been selected out of 4 SELRPN: 1 atoms have been selected out of 4 GEOM= 51.770473 X-PLOR>print angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. (TRYP 1 CA |TRYP 1 CB |TRYP 1 CG ) 109.558 109.500 0.058 0.001 500.000 (TRYP 1 CB |TRYP 1 CG |TRYP 1 CD1 ) 124.767 125.000 -0.233 0.008 500.000 RMS deviation= 0.170 X-PLOR>print bonds (atom-i |atom-j ) dist. equil. delta energy const. (TRYP 1 CA |TRYP 1 CB ) 1.530 1.530 0.000 0.000 1000.000 (TRYP 1 CB |TRYP 1 CG ) 1.496 1.495 0.001 0.000 1000.000 (TRYP 1 CG |TRYP 1 CD1 ) 1.353 1.352 0.001 0.000 1000.000 RMS deviation= 0.000 X-PLOR> X-PLOR> X-PLOR>{* =============================================================== *} X-PLOR>{* test 4: test coordinate reference *} X-PLOR>{* =============================================================== *} X-PLOR> X-PLOR>structure reset end SCRATC-warning: RESTraints DIHEdral database 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= 0) NACC= 0(MAXPAD= 0) NNB= 0(MAXNB= 100) 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>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>flags FLAGS> exclude * include bond dihe angl impr vdw FLAGS>end X-PLOR> X-PLOR>{* delete everything except Ca and substituents *} X-PLOR>delete selection=( not SELRPN> ( name ca or name cb or name c or name n or name ha ) ) end SELRPN: 22 atoms have been selected out of 27 MAPIC: Atom numbers being modified XPLOR: current counts (number in parenthesis is maximum) NATOM= 5(MAXA= 200) NBOND= 4(MAXB= 100) NTHETA= 6(MAXT= 100) NGRP= 3(MAXGRP= 100) NPHI= 0(MAXP= 100) NIMPHI= 1(MAXIMP= 100) NDON= 0(MAXPAD= 0) NACC= 0(MAXPAD= 0) NNB= 0(MAXNB= 100) X-PLOR> X-PLOR>vector do (x=x+4.) ( name ha ) SELRPN: 1 atoms have been selected out of 5 X-PLOR> X-PLOR>coor copy end COOR: selected main coordinates copied to comp X-PLOR> X-PLOR>mmdg MMDG> reference=parameters MMDG> verbose off MMDG> iacc=0.01 tacc=0.01 bacc=0.001 pacc=0.01 MMDG> random MMDG> metrize (all) 100 SELRPN: 5 atoms have been selected out of 5 MMDG>end MMDG: 5 atoms will be randomly metrized. DGSETNX: found 20 exclusions (1--2, 1--3) for repulsive lower bounds. TRYP 1 CB TRYP 1 HA 2.1173 2.1313 2.1455 * * Geometric inconsistency--lower bound greater than upper. Attempted to continue by inverting these bounds. %DISGEO-ERR: There are geometric inconsistencies. Proceed at own risk. X-PLOR> X-PLOR>set mess=off end coor fit end set mess=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 1.3942 X-PLOR>coor rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 1.394201, square sum= 9.7190, denominator= 5.0000 X-PLOR>vector do (z=-z) ( all ) SELRPN: 5 atoms have been selected out of 5 X-PLOR>set mess=off end coor fit end set mess=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 1.7907 X-PLOR>coor rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 1.790702, square sum= 16.0331, denominator= 5.0000 X-PLOR>coor swap end COOR: selected coordinates swaped (main<->comp) X-PLOR>coor copy end COOR: selected main coordinates copied to comp X-PLOR> X-PLOR>vector do (refx=x ) ( all ) SELRPN: 5 atoms have been selected out of 5 X-PLOR>vector do (refy=y) ( all ) SELRPN: 5 atoms have been selected out of 5 X-PLOR>vector do (refz=z) ( all ) SELRPN: 5 atoms have been selected out of 5 X-PLOR>mmdg MMDG> reference=coordinates MMDG> verbose off MMDG> iacc=0.01 tacc=0.01 bacc=0.001 pacc=0.01 MMDG> random MMDG> metrize (all) 100 SELRPN: 5 atoms have been selected out of 5 MMDG>end MMDG: 5 atoms will be randomly metrized. DGSETNX: found 20 exclusions (1--2, 1--3) for repulsive lower bounds. X-PLOR> X-PLOR>set mess=off end coor fit end set mess=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 0.0009 X-PLOR>coor rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.000945, square sum= 0.0000, denominator= 5.0000 X-PLOR>vector do (z=-z) ( all ) SELRPN: 5 atoms have been selected out of 5 X-PLOR>set mess=off end coor fit end set mess=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 0.8697 X-PLOR>coor rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.869689, square sum= 3.7818, denominator= 5.0000 X-PLOR>if ( $RESULT > 0.1 ) then NEXTCD: condition evaluated as true X-PLOR> vector do (z=-z) ( all ) SELRPN: 5 atoms have been selected out of 5 X-PLOR>end if X-PLOR> X-PLOR>print angles (atom-i |atom-j |atom-k ) angle equil. delta energy const. (TRYP 1 N |TRYP 1 CA |TRYP 1 HA ) 108.595 109.500 -0.905 0.125 500.000 (TRYP 1 N |TRYP 1 CA |TRYP 1 CB ) 111.135 104.000 7.135 7.754 500.000 (TRYP 1 N |TRYP 1 CA |TRYP 1 C ) 108.520 109.500 -0.980 0.146 500.000 (TRYP 1 HA |TRYP 1 CA |TRYP 1 CB ) 51.524 109.500 -57.976 511.946 500.000 (TRYP 1 HA |TRYP 1 CA |TRYP 1 C ) 142.477 109.500 32.977 165.637 500.000 (TRYP 1 CB |TRYP 1 CA |TRYP 1 C ) 108.635 109.500 -0.865 0.114 500.000 RMS deviation= 27.393 X-PLOR>print impropers (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period (TRYP 1 HA |TRYP 1 N |TRYP 1 C |TRYP 1 CB ) 30.644 65.977 35.333 190.148 500.000 0 RMS deviation= 35.333 X-PLOR>print dihedrals (atom-i |atom-j |atom-k |atom-L ) angle equil. delta energy const. period X-PLOR> X-PLOR>stop HEAP: maximum use= 1141130 current use= 1110871 X-PLOR: total CPU time= 0.1900 s X-PLOR: entry time at 17:23:34 7-Sep-06 X-PLOR: exit time at 17:23:34 7-Sep-06