XPLOR-NIH version 2.19 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: 24-Jan-08 16:50:15 X-PLOR>remarks dgtest1.inp X-PLOR>remarks test metric matrix distrance geometry module -- X-PLOR>remarks basic tests on a TRP amino acid 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>topology RTFRDR> RTFRDR> pres dimp RESIDUE> delete improper HB1 HB2 CA CG RESIDUE> delete improper HT1 HT2 CA HT3 RESIDUE> end RTFRDR>end X-PLOR> X-PLOR>patch dimp reference=nil=( all ) end SELRPN: 27 atoms have been selected out of 27 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= 21(MAXIMP= 100) NDON= 0(MAXPAD= 0) NACC= 0(MAXPAD= 0) NNB= 6(MAXNB= 100) X-PLOR> X-PLOR>coor copy end COOR: selected main coordinates copied to comp X-PLOR> X-PLOR>flags include noe cdih end X-PLOR> X-PLOR>{* scale the energies to reduce precision dependencies of the output *} X-PLOR>constraints CONS> interaction ( all ) ( all ) SELRPN: 27 atoms have been selected out of 27 SELRPN: 27 atoms have been selected out of 27 CONS> weight bond 0.001 WEIGHT> angl 0.001 WEIGHT> impr 0.001 WEIGHT> dihe 0.001 WEIGHT> vdw 0.001 WEIGHT> elec 0.001 WEIGHT> end CONS>end X-PLOR> X-PLOR>energy end MAKINB: mode 5 found 138 exclusions, 59 interactions(1-4) and 79 GB exclusions --------------- cycle= 1 -------------------------------------------------- | Etotal =0.022 grad(E)=0.020 E(BOND)=0.007 E(ANGL)=0.015 | | E(DIHE)=0.000 E(IMPR)=0.000 E(VDW )=0.000 E(ELEC)=0.000 | | E(CDIH)=0.000 E(NOE )=0.000 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>{* =============================================================== *} X-PLOR>{* test 1: generate all possible distances and store as NOEs *} X-PLOR>{* =============================================================== *} X-PLOR>set display prenoes.dat end ASSFIL: file /home/schwitrs/xplor-bzr/test/prenoes.dat opened. X-PLOR> X-PLOR>set message=off end X-PLOR>set echo=off end NOE: allocating space for 2000 restraints. X-PLOR> X-PLOR>set seed=12345 end X-PLOR> X-PLOR>mmdg MMDG> verbose off MMDG> iacc=5. tacc=5. bacc=0.2 pacc=5. MMDG> random MMDG> metrize (all) 100 SELRPN: 27 atoms have been selected out of 27 MMDG>end MMDG: 27 atoms will be randomly metrized. DGSETNX: found 152 exclusions (1--2, 1--3) for repulsive lower bounds. X-PLOR> X-PLOR>set display=OUTPUT end X-PLOR>display $embedded TRUE X-PLOR>display $non_met_gap 0 X-PLOR>display $dgscale 1.00006 X-PLOR> X-PLOR>vector do (x = x * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (y = y * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (z = z * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR> X-PLOR>energy end --------------- cycle= 2 -------------------------------------------------- | Etotal =2.933 grad(E)=2.859 E(BOND)=0.006 E(ANGL)=0.015 | | E(DIHE)=0.000 E(IMPR)=2.662 E(VDW )=0.000 E(ELEC)=0.000 | | E(CDIH)=0.000 E(NOE )=0.249 | ------------------------------------------------------------------------------- X-PLOR>evaluate ($chi_ener=$impr) EVALUATE: symbol $CHI_ENER set to 2.66213 (real) X-PLOR>vector do (z=-z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>energy end --------------- cycle= 3 -------------------------------------------------- | Etotal =0.272 grad(E)=2.860 E(BOND)=0.006 E(ANGL)=0.015 | | E(DIHE)=0.000 E(IMPR)=0.001 E(VDW )=0.000 E(ELEC)=0.000 | | E(CDIH)=0.000 E(NOE )=0.249 | ------------------------------------------------------------------------------- X-PLOR>if ($impr > $chi_ener) then NEXTCD: condition evaluated as false X-PLOR> vector do (z=-z) ( all ) X-PLOR>end if X-PLOR> X-PLOR>set message=off end coor fit end set message=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 0.0059 X-PLOR>coor rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.005945, square sum= 0.0010, denominator= 27.0000 X-PLOR>vector do (b=rmsd ) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>write coords end REMARK FILENAME="stdout" REMARK file parallhdg.pro REMARK NOTE: these parameters are DEPRECATED. Please instead use protein.par. REMARK geometric energy function parameters for distance geometry and REMARK simulated annealing. REMARK DATE:24-Jan-08 16:50:15 created by user: schwitrs ATOM 1 CA TRP 1 1.332 1.248 0.098 1.00 0.00 TRYP ATOM 2 HA TRP 1 1.572 0.786 1.041 1.00 0.01 TRYP ATOM 3 CB TRP 1 2.535 2.081 -0.420 1.00 0.00 TRYP ATOM 4 HB1 TRP 1 2.234 2.581 -1.324 1.00 0.01 TRYP ATOM 5 HB2 TRP 1 2.748 2.852 0.311 1.00 0.01 TRYP ATOM 6 CG TRP 1 3.803 1.234 -0.668 1.00 0.00 TRYP ATOM 7 CD1 TRP 1 4.717 0.870 0.298 1.00 0.00 TRYP ATOM 8 HD1 TRP 1 4.660 1.094 1.357 1.00 0.01 TRYP ATOM 9 CD2 TRP 1 4.352 0.652 -1.934 1.00 0.00 TRYP ATOM 10 NE1 TRP 1 5.722 0.120 -0.275 1.00 0.00 TRYP ATOM 11 HE1 TRP 1 6.485 -0.269 0.218 1.00 0.01 TRYP ATOM 12 CE2 TRP 1 5.559 -0.033 -1.632 1.00 0.00 TRYP ATOM 13 CE3 TRP 1 3.936 0.645 -3.303 1.00 0.00 TRYP ATOM 14 HE3 TRP 1 3.030 1.139 -3.601 1.00 0.00 TRYP ATOM 15 CZ2 TRP 1 6.310 -0.687 -2.611 1.00 0.00 TRYP ATOM 16 HZ2 TRP 1 7.212 -1.203 -2.341 1.00 0.01 TRYP ATOM 17 CZ3 TRP 1 4.696 -0.015 -4.280 1.00 0.01 TRYP ATOM 18 HZ3 TRP 1 4.370 -0.012 -5.307 1.00 0.00 TRYP ATOM 19 CH2 TRP 1 5.882 -0.675 -3.934 1.00 0.01 TRYP ATOM 20 HH2 TRP 1 6.463 -1.184 -4.688 1.00 0.01 TRYP ATOM 21 C TRP 1 0.137 2.182 0.303 1.00 0.00 TRYP ATOM 22 OT1 TRP 1 -0.628 2.347 -0.631 1.00 0.00 TRYP ATOM 23 OT2 TRP 1 0.011 2.721 1.386 1.00 0.01 TRYP ATOM 24 N TRP 1 0.945 0.192 -0.890 1.00 0.01 TRYP ATOM 25 HT1 TRP 1 1.559 -0.633 -0.770 1.00 0.01 TRYP ATOM 26 HT2 TRP 1 1.056 0.566 -1.857 1.00 0.01 TRYP ATOM 27 HT3 TRP 1 -0.047 -0.078 -0.739 1.00 0.00 TRYP END X-PLOR> 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>{* =============================================================== *} X-PLOR>{* test 2: generate all non-h distances and store as NOEs *} X-PLOR>{* =============================================================== *} X-PLOR>set display prenoes.dat end ASSFIL: file /home/schwitrs/xplor-bzr/test/prenoes.dat opened. X-PLOR> X-PLOR>set message=off end X-PLOR>set echo=off end NOE: allocating space for 2000 restraints. X-PLOR> X-PLOR>set seed=12345 end X-PLOR> X-PLOR>mmdg MMDG> verbose off MMDG> iacc=5. tacc=5. bacc=0.2 pacc=5. MMDG> random MMDG> metrize (all) 100 SELRPN: 27 atoms have been selected out of 27 MMDG>end MMDG: 27 atoms will be randomly metrized. DGSETNX: found 152 exclusions (1--2, 1--3) for repulsive lower bounds. X-PLOR> X-PLOR>set display=OUTPUT end X-PLOR>display $embedded TRUE X-PLOR>display $non_met_gap 0 X-PLOR>display $dgscale 1.04714 X-PLOR> X-PLOR>vector do (x = x * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (y = y * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (z = z * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR> X-PLOR>energy end --------------- cycle= 4 -------------------------------------------------- | Etotal =408.031 grad(E)=109.555 E(BOND)=3.228 E(ANGL)=7.311 | | E(DIHE)=0.000 E(IMPR)=11.856 E(VDW )=5.836 E(ELEC)=0.000 | | E(CDIH)=0.000 E(NOE )=379.800 | ------------------------------------------------------------------------------- X-PLOR>evaluate ($chi_ener=$impr) EVALUATE: symbol $CHI_ENER set to 11.8562 (real) X-PLOR>vector do (z=-z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>energy end --------------- cycle= 5 -------------------------------------------------- | Etotal =409.674 grad(E)=109.528 E(BOND)=3.228 E(ANGL)=7.311 | | E(DIHE)=0.000 E(IMPR)=13.499 E(VDW )=5.836 E(ELEC)=0.000 | | E(CDIH)=0.000 E(NOE )=379.800 | ------------------------------------------------------------------------------- X-PLOR>if ($impr > $chi_ener) then NEXTCD: condition evaluated as true X-PLOR> vector do (z=-z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>end if X-PLOR> X-PLOR>set mess=off end coor fit sele=( not hydro ) end set mess=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 0.3338 X-PLOR>coor rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 1.137723, square sum= 34.9492, denominator= 27.0000 X-PLOR>vector do (b=rmsd ) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>write coords end REMARK FILENAME="stdout" REMARK file parallhdg.pro REMARK NOTE: these parameters are DEPRECATED. Please instead use protein.par. REMARK geometric energy function parameters for distance geometry and REMARK simulated annealing. REMARK DATE:24-Jan-08 16:50:15 created by user: schwitrs ATOM 1 CA TRP 1 1.301 1.477 0.184 1.00 0.25 TRYP ATOM 2 HA TRP 1 1.896 1.220 0.412 1.00 0.83 TRYP ATOM 3 CB TRP 1 2.550 2.417 -0.621 1.00 0.39 TRYP ATOM 4 HB1 TRP 1 2.544 1.962 -2.035 1.00 1.00 TRYP ATOM 5 HB2 TRP 1 2.777 2.500 -1.126 1.00 1.48 TRYP ATOM 6 CG TRP 1 3.934 1.486 -0.482 1.00 0.34 TRYP ATOM 7 CD1 TRP 1 4.795 0.897 0.323 1.00 0.09 TRYP ATOM 8 HD1 TRP 1 3.996 -0.401 -0.015 1.00 2.14 TRYP ATOM 9 CD2 TRP 1 4.538 0.647 -1.624 1.00 0.37 TRYP ATOM 10 NE1 TRP 1 5.640 -0.039 -0.255 1.00 0.18 TRYP ATOM 11 HE1 TRP 1 5.407 -0.902 -0.412 1.00 1.40 TRYP ATOM 12 CE2 TRP 1 5.632 -0.045 -1.839 1.00 0.22 TRYP ATOM 13 CE3 TRP 1 3.990 0.703 -3.407 1.00 0.13 TRYP ATOM 14 HE3 TRP 1 3.574 1.286 -3.115 1.00 0.75 TRYP ATOM 15 CZ2 TRP 1 6.106 -1.220 -2.872 1.00 0.63 TRYP ATOM 16 HZ2 TRP 1 4.197 -1.750 -3.350 1.00 3.23 TRYP ATOM 17 CZ3 TRP 1 4.816 0.262 -4.424 1.00 0.34 TRYP ATOM 18 HZ3 TRP 1 4.714 1.340 -3.684 1.00 2.14 TRYP ATOM 19 CH2 TRP 1 6.165 -0.815 -3.974 1.00 0.32 TRYP ATOM 20 HH2 TRP 1 5.824 0.157 -3.163 1.00 2.13 TRYP ATOM 21 C TRP 1 -0.007 2.242 0.265 1.00 0.16 TRYP ATOM 22 OT1 TRP 1 -0.773 2.055 -0.402 1.00 0.40 TRYP ATOM 23 OT2 TRP 1 -0.250 2.535 1.161 1.00 0.39 TRYP ATOM 24 N TRP 1 0.865 0.258 -0.519 1.00 0.39 TRYP ATOM 25 HT1 TRP 1 1.611 -0.125 0.108 1.00 1.02 TRYP ATOM 26 HT2 TRP 1 0.976 -0.025 -1.030 1.00 1.02 TRYP ATOM 27 HT3 TRP 1 0.737 -0.113 -0.683 1.00 0.79 TRYP END X-PLOR> 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>{* =============================================================== *} X-PLOR>{* test 3: use "realistic" NOE data set *} X-PLOR>{* =============================================================== *} X-PLOR>set display prenoes.dat end ASSFIL: file /home/schwitrs/xplor-bzr/test/prenoes.dat opened. X-PLOR> X-PLOR>set message=off end X-PLOR>set echo=off end NOE: allocating space for 2000 restraints. X-PLOR> X-PLOR>set seed=12345 end X-PLOR> X-PLOR>mmdg MMDG> verbose off MMDG> iacc=5. tacc=5. bacc=0.2 pacc=5. MMDG> random MMDG> metrize (all) 100 SELRPN: 27 atoms have been selected out of 27 MMDG>end MMDG: 27 atoms will be randomly metrized. DGSETNX: found 152 exclusions (1--2, 1--3) for repulsive lower bounds. X-PLOR> X-PLOR>set display=OUTPUT end X-PLOR>display $embedded TRUE X-PLOR>display $non_met_gap 0 X-PLOR>display $dgscale 1.12914 X-PLOR> X-PLOR>vector do (x = x * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (y = y * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (z = z * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR> X-PLOR>energy end %atoms "TRYP-1 -TRP -HB1 " and "TRYP-1 -TRP -HE3 " only 1.07 A apart %atoms "TRYP-1 -TRP -HB1 " and "TRYP-1 -TRP -OT1 " only 0.67 A apart %atoms "TRYP-1 -TRP -HB1 " and "TRYP-1 -TRP -OT2 " only 1.32 A apart %atoms "TRYP-1 -TRP -HE3 " and "TRYP-1 -TRP -OT1 " only 1.24 A apart --------------- cycle= 6 -------------------------------------------------- | Etotal =69.887 grad(E)=3.192 E(BOND)=5.654 E(ANGL)=14.042 | | E(DIHE)=0.000 E(IMPR)=19.668 E(VDW )=24.844 E(ELEC)=0.000 | | E(CDIH)=0.000 E(NOE )=5.679 | ------------------------------------------------------------------------------- X-PLOR>evaluate ($chi_ener=$impr) EVALUATE: symbol $CHI_ENER set to 19.6683 (real) X-PLOR>vector do (z=-z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>energy end %atoms "TRYP-1 -TRP -HB1 " and "TRYP-1 -TRP -HE3 " only 1.07 A apart %atoms "TRYP-1 -TRP -HB1 " and "TRYP-1 -TRP -OT1 " only 0.67 A apart %atoms "TRYP-1 -TRP -HB1 " and "TRYP-1 -TRP -OT2 " only 1.32 A apart %atoms "TRYP-1 -TRP -HE3 " and "TRYP-1 -TRP -OT1 " only 1.24 A apart --------------- cycle= 7 -------------------------------------------------- | Etotal =72.268 grad(E)=3.251 E(BOND)=5.654 E(ANGL)=14.042 | | E(DIHE)=0.000 E(IMPR)=22.050 E(VDW )=24.844 E(ELEC)=0.000 | | E(CDIH)=0.000 E(NOE )=5.679 | ------------------------------------------------------------------------------- X-PLOR>if ($impr > $chi_ener) then NEXTCD: condition evaluated as true X-PLOR> vector do (z=-z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>end if X-PLOR> X-PLOR>set message=off end coor fit end set message=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 1.9751 X-PLOR>coor rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 1.975090, square sum= 105.3265, denominator= 27.0000 X-PLOR>vector do (b=rmsd ) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>write coords end REMARK FILENAME="stdout" REMARK file parallhdg.pro REMARK NOTE: these parameters are DEPRECATED. Please instead use protein.par. REMARK geometric energy function parameters for distance geometry and REMARK simulated annealing. REMARK DATE:24-Jan-08 16:50:15 created by user: schwitrs ATOM 1 CA TRP 1 1.039 1.452 -0.263 1.00 0.51 TRYP ATOM 2 HA TRP 1 1.326 1.586 0.070 1.00 1.28 TRYP ATOM 3 CB TRP 1 2.692 1.591 -0.265 1.00 0.54 TRYP ATOM 4 HB1 TRP 1 2.495 1.518 -1.711 1.00 1.17 TRYP ATOM 5 HB2 TRP 1 2.805 1.770 0.114 1.00 1.10 TRYP ATOM 6 CG TRP 1 4.125 1.728 -0.008 1.00 0.89 TRYP ATOM 7 CD1 TRP 1 5.466 2.453 -0.016 1.00 1.78 TRYP ATOM 8 HD1 TRP 1 4.907 1.365 0.174 1.00 1.24 TRYP ATOM 9 CD2 TRP 1 4.921 1.383 -0.903 1.00 1.39 TRYP ATOM 10 NE1 TRP 1 5.528 0.207 -0.016 1.00 0.34 TRYP ATOM 11 HE1 TRP 1 5.469 -0.705 -0.369 1.00 1.25 TRYP ATOM 12 CE2 TRP 1 5.522 -0.252 -1.645 1.00 0.22 TRYP ATOM 13 CE3 TRP 1 3.779 0.696 -2.321 1.00 1.00 TRYP ATOM 14 HE3 TRP 1 3.482 1.357 -2.103 1.00 1.58 TRYP ATOM 15 CZ2 TRP 1 4.652 -1.134 -2.522 1.00 1.72 TRYP ATOM 16 HZ2 TRP 1 3.339 -1.431 -3.174 1.00 3.98 TRYP ATOM 17 CZ3 TRP 1 3.755 1.585 -3.635 1.00 1.97 TRYP ATOM 18 HZ3 TRP 1 3.930 1.930 -3.024 1.00 3.03 TRYP ATOM 19 CH2 TRP 1 4.973 0.000 -3.840 1.00 1.14 TRYP ATOM 20 HH2 TRP 1 4.856 0.004 -2.824 1.00 2.73 TRYP ATOM 21 C TRP 1 1.327 1.611 -1.078 1.00 1.91 TRYP ATOM 22 OT1 TRP 1 2.481 2.096 -2.055 1.00 3.43 TRYP ATOM 23 OT2 TRP 1 1.825 1.842 -2.801 1.00 4.65 TRYP ATOM 24 N TRP 1 1.111 -1.046 -0.355 1.00 1.37 TRYP ATOM 25 HT1 TRP 1 2.202 -1.004 0.353 1.00 1.35 TRYP ATOM 26 HT2 TRP 1 1.301 -1.159 -0.978 1.00 1.96 TRYP ATOM 27 HT3 TRP 1 1.346 -0.926 -1.000 1.00 1.65 TRYP END X-PLOR> 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>{* =============================================================== *} X-PLOR>{* test 4: test the "rigid" group option *} X-PLOR>{* =============================================================== *} X-PLOR> X-PLOR>set seed=12345 end X-PLOR> X-PLOR>mmdg MMDG> verbose off MMDG> iacc=5. tacc=5. bacc=0.2 pacc=5. MMDG> group=( all ) 0.1 SELRPN: 27 atoms have been selected out of 27 MMDG> random MMDG> metrize (all) 100 SELRPN: 27 atoms have been selected out of 27 MMDG>end MMDG: 27 atoms will be randomly metrized. DGSETNX: found 152 exclusions (1--2, 1--3) for repulsive lower bounds. X-PLOR> X-PLOR>set display=OUTPUT end X-PLOR>display $embedded TRUE X-PLOR>display $non_met_gap 0 X-PLOR>display $dgscale 1.00193 X-PLOR> X-PLOR>vector do (x = x * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (y = y * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (z = z * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR> X-PLOR>energy end --------------- cycle= 8 -------------------------------------------------- | Etotal =3.706 grad(E)=0.463 E(BOND)=0.036 E(ANGL)=0.056 | | E(DIHE)=0.000 E(IMPR)=2.639 E(VDW )=0.000 E(ELEC)=0.000 | | E(CDIH)=0.000 E(NOE )=0.976 | ------------------------------------------------------------------------------- X-PLOR>evaluate ($chi_ener=$impr) EVALUATE: symbol $CHI_ENER set to 2.63868 (real) X-PLOR>vector do (z=-z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>energy end --------------- cycle= 9 -------------------------------------------------- | Etotal =1.095 grad(E)=0.446 E(BOND)=0.036 E(ANGL)=0.056 | | E(DIHE)=0.000 E(IMPR)=0.028 E(VDW )=0.000 E(ELEC)=0.000 | | E(CDIH)=0.000 E(NOE )=0.976 | ------------------------------------------------------------------------------- X-PLOR>if ($impr > $chi_ener) then NEXTCD: condition evaluated as false X-PLOR> vector do (z=-z) ( all ) X-PLOR>end if X-PLOR> X-PLOR>set message=off end coor fit end set message=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 0.0601 X-PLOR>coor rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 0.060101, square sum= 0.0975, denominator= 27.0000 X-PLOR>vector do (b=rmsd ) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>write coords end REMARK FILENAME="stdout" REMARK file parallhdg.pro REMARK NOTE: these parameters are DEPRECATED. Please instead use protein.par. REMARK geometric energy function parameters for distance geometry and REMARK simulated annealing. REMARK DATE:24-Jan-08 16:50:15 created by user: schwitrs ATOM 1 CA TRP 1 1.335 1.266 0.120 1.00 0.03 TRYP ATOM 2 HA TRP 1 1.582 0.838 1.063 1.00 0.06 TRYP ATOM 3 CB TRP 1 2.547 2.055 -0.432 1.00 0.03 TRYP ATOM 4 HB1 TRP 1 2.187 2.539 -1.378 1.00 0.09 TRYP ATOM 5 HB2 TRP 1 2.724 2.872 0.275 1.00 0.05 TRYP ATOM 6 CG TRP 1 3.789 1.288 -0.658 1.00 0.06 TRYP ATOM 7 CD1 TRP 1 4.722 0.903 0.285 1.00 0.04 TRYP ATOM 8 HD1 TRP 1 4.669 1.049 1.370 1.00 0.05 TRYP ATOM 9 CD2 TRP 1 4.354 0.647 -1.898 1.00 0.04 TRYP ATOM 10 NE1 TRP 1 5.697 0.104 -0.269 1.00 0.03 TRYP ATOM 11 HE1 TRP 1 6.482 -0.387 0.268 1.00 0.14 TRYP ATOM 12 CE2 TRP 1 5.577 -0.006 -1.661 1.00 0.05 TRYP ATOM 13 CE3 TRP 1 3.923 0.648 -3.303 1.00 0.02 TRYP ATOM 14 HE3 TRP 1 3.056 1.129 -3.577 1.00 0.04 TRYP ATOM 15 CZ2 TRP 1 6.319 -0.655 -2.642 1.00 0.05 TRYP ATOM 16 HZ2 TRP 1 7.151 -1.236 -2.378 1.00 0.09 TRYP ATOM 17 CZ3 TRP 1 4.664 0.040 -4.298 1.00 0.07 TRYP ATOM 18 HZ3 TRP 1 4.373 0.007 -5.297 1.00 0.02 TRYP ATOM 19 CH2 TRP 1 5.914 -0.647 -3.955 1.00 0.05 TRYP ATOM 20 HH2 TRP 1 6.513 -1.173 -4.667 1.00 0.06 TRYP ATOM 21 C TRP 1 0.116 2.181 0.303 1.00 0.02 TRYP ATOM 22 OT1 TRP 1 -0.619 2.359 -0.627 1.00 0.02 TRYP ATOM 23 OT2 TRP 1 0.037 2.761 1.319 1.00 0.09 TRYP ATOM 24 N TRP 1 0.945 0.146 -0.855 1.00 0.07 TRYP ATOM 25 HT1 TRP 1 1.598 -0.616 -0.731 1.00 0.06 TRYP ATOM 26 HT2 TRP 1 1.042 0.508 -1.842 1.00 0.07 TRYP ATOM 27 HT3 TRP 1 -0.043 -0.099 -0.732 1.00 0.03 TRYP END X-PLOR> 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>{* =============================================================== *} X-PLOR>{* test 4b: test the "rigid" group option with two groups *} X-PLOR>{* =============================================================== *} X-PLOR> X-PLOR>set seed=12345 end X-PLOR> X-PLOR>mmdg MMDG> verbose off MMDG> iacc=5. tacc=5. bacc=0.2 pacc=5. MMDG> group=( not hydrogen ) 0.1 SELRPN: 15 atoms have been selected out of 27 MMDG> group=( hydrogen ) 0.1 SELRPN: 12 atoms have been selected out of 27 MMDG> random MMDG> metrize (all) 100 SELRPN: 27 atoms have been selected out of 27 MMDG>end MMDG: 27 atoms will be randomly metrized. DGSETNX: found 152 exclusions (1--2, 1--3) for repulsive lower bounds. X-PLOR> X-PLOR>set display=OUTPUT end X-PLOR>display $embedded TRUE X-PLOR>display $non_met_gap 0 X-PLOR>display $dgscale 1.01336 X-PLOR> X-PLOR>vector do (x = x * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (y = y * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (z = z * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR> X-PLOR>energy end %atoms "TRYP-1 -TRP -HB1 " and "TRYP-1 -TRP -HT2 " only 1.32 A apart --------------- cycle= 10 -------------------------------------------------- | Etotal =25.366 grad(E)=1.741 E(BOND)=7.980 E(ANGL)=3.766 | | E(DIHE)=0.000 E(IMPR)=3.992 E(VDW )=7.945 E(ELEC)=0.000 | | E(CDIH)=0.000 E(NOE )=1.682 | ------------------------------------------------------------------------------- X-PLOR>evaluate ($chi_ener=$impr) EVALUATE: symbol $CHI_ENER set to 3.99229 (real) X-PLOR>vector do (z=-z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>energy end %atoms "TRYP-1 -TRP -HB1 " and "TRYP-1 -TRP -HT2 " only 1.32 A apart --------------- cycle= 11 -------------------------------------------------- | Etotal =26.465 grad(E)=1.742 E(BOND)=7.980 E(ANGL)=3.766 | | E(DIHE)=0.000 E(IMPR)=5.092 E(VDW )=7.945 E(ELEC)=0.000 | | E(CDIH)=0.000 E(NOE )=1.682 | ------------------------------------------------------------------------------- X-PLOR>if ($impr > $chi_ener) then NEXTCD: condition evaluated as true X-PLOR> vector do (z=-z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>end if X-PLOR> X-PLOR>coor fit sele=( not hydro ) end SELRPN: 15 atoms have been selected out of 27 COOR: using atom subset. Fitted coordinate set r' related to original set r by r'=R*r + T This transformation is applied to all coordinates. Translation vector T = ( 3.2301 0.9676 -1.3246) Rotation matrix = -0.810997 0.580128 0.075733 0.094681 0.002402 0.995505 0.577338 0.814522 -0.056875 Corresp. Eulerian angles (theta1,theta2,theta3) 144.6708 93.2605 4.3504 Corresp. spherical polar angles (psi,phi,kappa) 134.0740 110.4463 201.1347 Corresp. rotation angle 158.8653 about axis 0.2510 0.6956 0.6732 Corresp. quaternions 0.1834 0.2467 0.6838 0.6618 R.m.s. diff. between fitted set and comp. set for selected atoms = 0.7839 X-PLOR>coor rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 1.621528, square sum= 70.9925, denominator= 27.0000 X-PLOR>vector do (b=rmsd ) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>write coords end REMARK FILENAME="stdout" REMARK file parallhdg.pro REMARK NOTE: these parameters are DEPRECATED. Please instead use protein.par. REMARK geometric energy function parameters for distance geometry and REMARK simulated annealing. REMARK DATE:24-Jan-08 16:50:15 created by user: schwitrs ATOM 1 CA TRP 1 1.502 1.303 0.624 1.00 0.56 TRYP ATOM 2 HA TRP 1 1.391 0.947 1.262 1.00 0.33 TRYP ATOM 3 CB TRP 1 2.105 0.363 -0.010 1.00 1.82 TRYP ATOM 4 HB1 TRP 1 1.646 -0.106 -0.978 1.00 2.78 TRYP ATOM 5 HB2 TRP 1 2.203 -0.024 0.724 1.00 2.95 TRYP ATOM 6 CG TRP 1 3.516 0.366 -0.415 1.00 0.94 TRYP ATOM 7 CD1 TRP 1 4.558 0.645 0.291 1.00 0.27 TRYP ATOM 8 HD1 TRP 1 4.436 1.296 1.378 1.00 0.30 TRYP ATOM 9 CD2 TRP 1 4.412 0.290 -1.670 1.00 0.46 TRYP ATOM 10 NE1 TRP 1 5.685 0.439 -0.406 1.00 0.34 TRYP ATOM 11 HE1 TRP 1 6.448 1.766 0.074 1.00 2.03 TRYP ATOM 12 CE2 TRP 1 5.684 0.292 -1.808 1.00 0.39 TRYP ATOM 13 CE3 TRP 1 3.804 -0.021 -3.139 1.00 0.70 TRYP ATOM 14 HE3 TRP 1 2.733 -0.029 -3.455 1.00 1.21 TRYP ATOM 15 CZ2 TRP 1 6.467 0.172 -3.022 1.00 0.97 TRYP ATOM 16 HZ2 TRP 1 6.548 3.238 -2.965 1.00 4.53 TRYP ATOM 17 CZ3 TRP 1 4.596 -0.271 -4.254 1.00 0.27 TRYP ATOM 18 HZ3 TRP 1 3.828 1.496 -5.309 1.00 1.60 TRYP ATOM 19 CH2 TRP 1 6.192 -0.045 -4.185 1.00 0.75 TRYP ATOM 20 HH2 TRP 1 6.132 2.192 -4.987 1.00 3.41 TRYP ATOM 21 C TRP 1 0.085 2.368 0.094 1.00 0.29 TRYP ATOM 22 OT1 TRP 1 -0.298 2.878 -0.440 1.00 0.65 TRYP ATOM 23 OT2 TRP 1 -0.075 3.452 0.521 1.00 1.14 TRYP ATOM 24 N TRP 1 1.071 0.631 -0.664 1.00 0.51 TRYP ATOM 25 HT1 TRP 1 1.589 1.473 -0.544 1.00 2.12 TRYP ATOM 26 HT2 TRP 1 0.840 0.606 -1.746 1.00 0.25 TRYP ATOM 27 HT3 TRP 1 0.115 0.409 -0.734 1.00 0.51 TRYP END X-PLOR> 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>{* =============================================================== *} X-PLOR>{* test 4c: test substructures *} X-PLOR>{* =============================================================== *} X-PLOR> X-PLOR>set seed=12345 end X-PLOR> X-PLOR>vector do (refx=x) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (refy=y) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (refz=z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR> X-PLOR>mmdg MMDG> verbose off MMDG> iacc=5. tacc=5. bacc=0.2 pacc=5. MMDG> group=( not hydrogen ) 0.01 SELRPN: 15 atoms have been selected out of 27 MMDG> group=( hydrogen ) 0.01 SELRPN: 12 atoms have been selected out of 27 MMDG> substructure=( not hydrogen ) SELRPN: 15 atoms have been selected out of 27 MMDG> random MMDG> metrize (all) 100 SELRPN: 27 atoms have been selected out of 27 MMDG>end DGSMOOT: number of connections: 476 DGSMOOT: using full matrix bound smoothing algorithm. MMDG: 15 atoms will be randomly metrized. DGSETNX: found 152 exclusions (1--2, 1--3) for repulsive lower bounds. DGNOMET: number of connections: 210 DGNOMET: using full matrix bound smoothing algorithm. X-PLOR> X-PLOR>set display=OUTPUT end X-PLOR>display $embedded TRUE X-PLOR>display $non_met_gap 0 X-PLOR>display $dgscale 0.99996 X-PLOR> X-PLOR>vector do (x = x * $dgscale) (not hydrogen) SELRPN: 15 atoms have been selected out of 27 X-PLOR>vector do (y = y * $dgscale) (not hydrogen) SELRPN: 15 atoms have been selected out of 27 X-PLOR>vector do (z = z * $dgscale) (not hydrogen) SELRPN: 15 atoms have been selected out of 27 X-PLOR> X-PLOR>set mess=off end coor fit sele=( not hydro ) end set mess=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 0.9414 X-PLOR> X-PLOR>vector do (z=-z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>set mess=off end coor fit sele=( not hydro ) end set mess=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 0.0127 X-PLOR> 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>{* =============================================================== *} X-PLOR>{* test 4d: test substructures with storage in memory *} X-PLOR>{* =============================================================== *} X-PLOR> X-PLOR>set seed=12345 end X-PLOR> X-PLOR>vector do (refx=x) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (refy=y) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (refz=z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR> X-PLOR>mmdg MMDG> verbose off MMDG> iacc=5. tacc=5. bacc=0.2 pacc=5. MMDG> group=( not hydrogen ) 0.01 SELRPN: 15 atoms have been selected out of 27 MMDG> group=( hydrogen ) 0.01 SELRPN: 12 atoms have been selected out of 27 MMDG> storebounds MMDG>end DGSMOOT: number of connections: 476 DGSMOOT: using full matrix bound smoothing algorithm. MMDG: storing smoothed bounds matrix in memory. No metrization or embedding performed. X-PLOR> X-PLOR>set seed=12345 end X-PLOR> X-PLOR>mmdg MMDG> recallbounds MMDG> substructure=( not hydrogen ) SELRPN: 15 atoms have been selected out of 27 MMDG> random MMDG> metrize (all) 100 SELRPN: 27 atoms have been selected out of 27 MMDG>end MMDG: 15 atoms will be randomly metrized. DGSETNX: found 152 exclusions (1--2, 1--3) for repulsive lower bounds. DGNOMET: number of connections: 210 DGNOMET: using full matrix bound smoothing algorithm. X-PLOR> X-PLOR>set display=OUTPUT end X-PLOR>display $embedded TRUE X-PLOR>display $non_met_gap 0 X-PLOR>display $dgscale 0.99996 X-PLOR> X-PLOR>vector do (x = x * $dgscale) (not hydrogen) SELRPN: 15 atoms have been selected out of 27 X-PLOR>vector do (y = y * $dgscale) (not hydrogen) SELRPN: 15 atoms have been selected out of 27 X-PLOR>vector do (z = z * $dgscale) (not hydrogen) SELRPN: 15 atoms have been selected out of 27 X-PLOR> X-PLOR>set mess=off end coor fit sele=( not hydro ) end set mess=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 0.9414 X-PLOR> X-PLOR>vector do (z=-z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>set mess=off end coor fit sele=( not hydro ) end set mess=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 0.0127 X-PLOR> X-PLOR>set seed=12345 end X-PLOR> X-PLOR>mmdg MMDG> recallbounds MMDG> substructure=( not hydrogen ) SELRPN: 15 atoms have been selected out of 27 MMDG> random MMDG> metrize (all) 100 SELRPN: 27 atoms have been selected out of 27 MMDG>end MMDG: 15 atoms will be randomly metrized. DGSETNX: found 152 exclusions (1--2, 1--3) for repulsive lower bounds. DGNOMET: number of connections: 210 DGNOMET: using full matrix bound smoothing algorithm. X-PLOR> X-PLOR>set display=OUTPUT end X-PLOR>display $embedded TRUE X-PLOR>display $non_met_gap 0 X-PLOR>display $dgscale 0.99996 X-PLOR> X-PLOR>vector do (x = x * $dgscale) (not hydrogen) SELRPN: 15 atoms have been selected out of 27 X-PLOR>vector do (y = y * $dgscale) (not hydrogen) SELRPN: 15 atoms have been selected out of 27 X-PLOR>vector do (z = z * $dgscale) (not hydrogen) SELRPN: 15 atoms have been selected out of 27 X-PLOR> X-PLOR>set mess=off end coor fit sele=( not hydro ) end set mess=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 0.9414 X-PLOR> X-PLOR>vector do (z=-z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>set mess=off end coor fit sele=( not hydro ) end set mess=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 0.0127 X-PLOR> 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> X-PLOR>{* =============================================================== *} X-PLOR>{* test 4e: test substructures with storage in file *} X-PLOR>{* =============================================================== *} X-PLOR> X-PLOR>set seed=12345 end X-PLOR> X-PLOR>vector do (refx=x) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (refy=y) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (refz=z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR> X-PLOR>mmdg MMDG> verbose off MMDG> iacc=5. tacc=5. bacc=0.2 pacc=5. MMDG> group=( not hydrogen ) 0.01 SELRPN: 15 atoms have been selected out of 27 MMDG> group=( hydrogen ) 0.01 SELRPN: 12 atoms have been selected out of 27 MMDG> writebounds=dgtest1.dat ASSFIL: file /home/schwitrs/xplor-bzr/test/dgtest1.dat opened. MMDG>end DGSMOOT: number of connections: 476 DGSMOOT: using full matrix bound smoothing algorithm. MMDG: writing smoothed bounds matrices to binary file. No metrization or embedding performed. X-PLOR> X-PLOR>set seed=12345 end X-PLOR> X-PLOR>mmdg MMDG> readbounds=dgtest1.dat ASSFIL: file /home/schwitrs/xplor-bzr/test/dgtest1.dat opened. MMDG> substructure=( not hydrogen ) SELRPN: 15 atoms have been selected out of 27 MMDG> random MMDG> metrize (all) 100 SELRPN: 27 atoms have been selected out of 27 MMDG>end MMDG: 15 atoms will be randomly metrized. DGSETNX: found 152 exclusions (1--2, 1--3) for repulsive lower bounds. DGNOMET: number of connections: 210 DGNOMET: using full matrix bound smoothing algorithm. X-PLOR> X-PLOR>set display=OUTPUT end X-PLOR>display $embedded TRUE X-PLOR>display $non_met_gap 0 X-PLOR>display $dgscale 0.99996 X-PLOR> X-PLOR>vector do (x = x * $dgscale) (not hydrogen) SELRPN: 15 atoms have been selected out of 27 X-PLOR>vector do (y = y * $dgscale) (not hydrogen) SELRPN: 15 atoms have been selected out of 27 X-PLOR>vector do (z = z * $dgscale) (not hydrogen) SELRPN: 15 atoms have been selected out of 27 X-PLOR> X-PLOR>set mess=off end coor fit sele=( not hydro ) end set mess=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 0.9414 X-PLOR> X-PLOR>vector do (z=-z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>set mess=off end coor fit sele=( not hydro ) end set mess=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 0.0127 X-PLOR> X-PLOR>set seed=12345 end X-PLOR> X-PLOR>mmdg MMDG> readbounds=dgtest1.dat MMDG> substructure=( not hydrogen ) SELRPN: 15 atoms have been selected out of 27 MMDG> random MMDG> metrize (all) 100 SELRPN: 27 atoms have been selected out of 27 MMDG>end MMDG: 15 atoms will be randomly metrized. DGSETNX: found 152 exclusions (1--2, 1--3) for repulsive lower bounds. DGNOMET: number of connections: 210 DGNOMET: using full matrix bound smoothing algorithm. X-PLOR> X-PLOR>set display=OUTPUT end X-PLOR>display $embedded TRUE X-PLOR>display $non_met_gap 0 X-PLOR>display $dgscale 0.99996 X-PLOR> X-PLOR>vector do (x = x * $dgscale) (not hydrogen) SELRPN: 15 atoms have been selected out of 27 X-PLOR>vector do (y = y * $dgscale) (not hydrogen) SELRPN: 15 atoms have been selected out of 27 X-PLOR>vector do (z = z * $dgscale) (not hydrogen) SELRPN: 15 atoms have been selected out of 27 X-PLOR> X-PLOR>set mess=off end coor fit sele=( not hydro ) end set mess=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 0.9414 X-PLOR> X-PLOR>vector do (z=-z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>set mess=off end coor fit sele=( not hydro ) end set mess=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 0.0127 X-PLOR> 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> X-PLOR>{* =============================================================== *} X-PLOR>{* test 5: test partial metrization *} X-PLOR>{* =============================================================== *} X-PLOR> X-PLOR>set seed=12345 end X-PLOR> X-PLOR>mmdg MMDG> verbose off MMDG> iacc=5. tacc=5. bacc=0.2 pacc=5. MMDG> random MMDG> metrize (all) 4 SELRPN: 27 atoms have been selected out of 27 MMDG>end MMDG: 4 atoms will be randomly metrized. DGSETNX: found 152 exclusions (1--2, 1--3) for repulsive lower bounds. DGNOMET: number of connections: 398 DGNOMET: using full matrix bound smoothing algorithm. X-PLOR> X-PLOR>set display=OUTPUT end X-PLOR>display $embedded TRUE X-PLOR>display $non_met_gap 2.07291 X-PLOR>display $dgscale 1.1068 X-PLOR> X-PLOR>vector do (x = x * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (y = y * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (z = z * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR> X-PLOR>energy end %atoms "TRYP-1 -TRP -CD2 " and "TRYP-1 -TRP -HH2 " only 0.80 A apart %atoms "TRYP-1 -TRP -HE3 " and "TRYP-1 -TRP -HH2 " only 1.44 A apart --------------- cycle= 12 -------------------------------------------------- | Etotal =129.761 grad(E)=13.311 E(BOND)=21.799 E(ANGL)=16.412 | | E(DIHE)=0.000 E(IMPR)=31.510 E(VDW )=28.124 E(ELEC)=0.000 | | E(CDIH)=0.000 E(NOE )=31.915 | ------------------------------------------------------------------------------- X-PLOR>evaluate ($chi_ener=$impr) EVALUATE: symbol $CHI_ENER set to 31.5104 (real) X-PLOR>vector do (z=-z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>energy end %atoms "TRYP-1 -TRP -CD2 " and "TRYP-1 -TRP -HH2 " only 0.80 A apart %atoms "TRYP-1 -TRP -HE3 " and "TRYP-1 -TRP -HH2 " only 1.44 A apart --------------- cycle= 13 -------------------------------------------------- | Etotal =129.031 grad(E)=13.321 E(BOND)=21.799 E(ANGL)=16.412 | | E(DIHE)=0.000 E(IMPR)=30.781 E(VDW )=28.124 E(ELEC)=0.000 | | E(CDIH)=0.000 E(NOE )=31.915 | ------------------------------------------------------------------------------- X-PLOR>if ($impr > $chi_ener) then NEXTCD: condition evaluated as false X-PLOR> vector do (z=-z) ( all ) X-PLOR>end if X-PLOR> X-PLOR>set message=off end coor fit end set message=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 2.4728 X-PLOR>coor rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 2.472779, square sum= 165.0952, denominator= 27.0000 X-PLOR>vector do (b=rmsd ) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>write coords end REMARK FILENAME="stdout" REMARK file parallhdg.pro REMARK NOTE: these parameters are DEPRECATED. Please instead use protein.par. REMARK geometric energy function parameters for distance geometry and REMARK simulated annealing. REMARK DATE:24-Jan-08 16:50:15 created by user: schwitrs ATOM 1 CA TRP 1 1.249 1.064 -0.173 1.00 0.33 TRYP ATOM 2 HA TRP 1 1.487 0.412 -0.821 1.00 1.90 TRYP ATOM 3 CB TRP 1 1.979 0.665 -0.851 1.00 1.59 TRYP ATOM 4 HB1 TRP 1 2.253 0.387 -2.068 1.00 2.32 TRYP ATOM 5 HB2 TRP 1 2.225 0.508 -0.668 1.00 2.59 TRYP ATOM 6 CG TRP 1 3.658 0.942 -0.586 1.00 0.33 TRYP ATOM 7 CD1 TRP 1 4.451 1.287 -0.030 1.00 0.60 TRYP ATOM 8 HD1 TRP 1 4.177 -1.012 1.118 1.00 2.18 TRYP ATOM 9 CD2 TRP 1 4.398 0.430 -1.714 1.00 0.32 TRYP ATOM 10 NE1 TRP 1 5.478 1.887 -1.092 1.00 1.96 TRYP ATOM 11 HE1 TRP 1 5.570 2.446 -0.536 1.00 2.95 TRYP ATOM 12 CE2 TRP 1 5.158 0.753 -2.081 1.00 0.99 TRYP ATOM 13 CE3 TRP 1 3.718 -1.343 -2.856 1.00 2.05 TRYP ATOM 14 HE3 TRP 1 4.286 -1.112 -1.543 1.00 3.30 TRYP ATOM 15 CZ2 TRP 1 6.493 0.890 -2.645 1.00 1.59 TRYP ATOM 16 HZ2 TRP 1 5.836 -0.045 -1.484 1.00 1.99 TRYP ATOM 17 CZ3 TRP 1 3.787 -0.880 -2.417 1.00 2.24 TRYP ATOM 18 HZ3 TRP 1 3.806 -0.977 -1.493 1.00 3.97 TRYP ATOM 19 CH2 TRP 1 4.227 0.029 -4.774 1.00 1.98 TRYP ATOM 20 HH2 TRP 1 4.141 0.058 -2.379 1.00 3.50 TRYP ATOM 21 C TRP 1 1.757 1.473 0.526 1.00 1.78 TRYP ATOM 22 OT1 TRP 1 3.314 2.299 0.405 1.00 4.08 TRYP ATOM 23 OT2 TRP 1 2.502 -0.735 0.362 1.00 4.38 TRYP ATOM 24 N TRP 1 1.278 3.723 -1.699 1.00 3.63 TRYP ATOM 25 HT1 TRP 1 1.371 2.073 -2.457 1.00 3.19 TRYP ATOM 26 HT2 TRP 1 1.948 2.602 -2.516 1.00 2.31 TRYP ATOM 27 HT3 TRP 1 0.105 0.696 -1.723 1.00 1.26 TRYP END X-PLOR> 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>{* =============================================================== *} X-PLOR>{* test 6: test ordered metrization *} X-PLOR>{* =============================================================== *} X-PLOR> X-PLOR>set seed=12345 end X-PLOR> X-PLOR>mmdg MMDG> verbose off MMDG> iacc=5. tacc=5. bacc=0.2 pacc=5. MMDG> ordered MMDG> metrize (all) 4 SELRPN: 27 atoms have been selected out of 27 MMDG>end MMDG: 4 atoms will be metrized in order. DGSETNX: found 152 exclusions (1--2, 1--3) for repulsive lower bounds. DGNOMET: number of connections: 382 DGNOMET: using full matrix bound smoothing algorithm. X-PLOR> X-PLOR>set display=OUTPUT end X-PLOR>display $embedded TRUE X-PLOR>display $non_met_gap 2.07366 X-PLOR>display $dgscale 1.06878 X-PLOR> X-PLOR>vector do (x = x * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (y = y * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (z = z * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR> X-PLOR>energy end %atoms "TRYP-1 -TRP -HB1 " and "TRYP-1 -TRP -HT2 " only 1.42 A apart %atoms "TRYP-1 -TRP -HB2 " and "TRYP-1 -TRP -HT1 " only 1.16 A apart --------------- cycle= 14 -------------------------------------------------- | Etotal =113.635 grad(E)=8.264 E(BOND)=16.994 E(ANGL)=11.172 | | E(DIHE)=0.000 E(IMPR)=19.695 E(VDW )=17.594 E(ELEC)=0.000 | | E(CDIH)=0.000 E(NOE )=48.180 | ------------------------------------------------------------------------------- X-PLOR>evaluate ($chi_ener=$impr) EVALUATE: symbol $CHI_ENER set to 19.6951 (real) X-PLOR>vector do (z=-z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>energy end %atoms "TRYP-1 -TRP -HB1 " and "TRYP-1 -TRP -HT2 " only 1.42 A apart %atoms "TRYP-1 -TRP -HB2 " and "TRYP-1 -TRP -HT1 " only 1.16 A apart --------------- cycle= 15 -------------------------------------------------- | Etotal =117.250 grad(E)=8.244 E(BOND)=16.994 E(ANGL)=11.172 | | E(DIHE)=0.000 E(IMPR)=23.310 E(VDW )=17.594 E(ELEC)=0.000 | | E(CDIH)=0.000 E(NOE )=48.180 | ------------------------------------------------------------------------------- X-PLOR>if ($impr > $chi_ener) then NEXTCD: condition evaluated as true X-PLOR> vector do (z=-z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>end if X-PLOR> X-PLOR>set message=off end coor fit end set message=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 2.2140 X-PLOR>coor rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 2.214027, square sum= 132.3518, denominator= 27.0000 X-PLOR>vector do (b=rmsd ) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>write coords end REMARK FILENAME="stdout" REMARK file parallhdg.pro REMARK NOTE: these parameters are DEPRECATED. Please instead use protein.par. REMARK geometric energy function parameters for distance geometry and REMARK simulated annealing. REMARK DATE:24-Jan-08 16:50:15 created by user: schwitrs ATOM 1 CA TRP 1 1.324 1.222 -1.368 1.00 1.46 TRYP ATOM 2 HA TRP 1 1.230 0.572 -1.749 1.00 2.82 TRYP ATOM 3 CB TRP 1 2.466 1.415 -1.047 1.00 0.92 TRYP ATOM 4 HB1 TRP 1 2.346 1.379 -0.807 1.00 1.32 TRYP ATOM 5 HB2 TRP 1 2.574 2.082 -1.196 1.00 1.70 TRYP ATOM 6 CG TRP 1 3.949 1.721 -0.851 1.00 0.54 TRYP ATOM 7 CD1 TRP 1 4.388 1.913 -0.058 1.00 1.15 TRYP ATOM 8 HD1 TRP 1 4.026 0.133 0.646 1.00 1.36 TRYP ATOM 9 CD2 TRP 1 4.996 1.763 -1.548 1.00 1.34 TRYP ATOM 10 NE1 TRP 1 5.779 1.771 0.062 1.00 1.68 TRYP ATOM 11 HE1 TRP 1 5.975 -0.016 1.512 1.00 1.42 TRYP ATOM 12 CE2 TRP 1 5.446 0.702 -1.091 1.00 0.92 TRYP ATOM 13 CE3 TRP 1 4.858 0.613 -3.110 1.00 0.94 TRYP ATOM 14 HE3 TRP 1 3.545 -0.029 -2.132 1.00 1.95 TRYP ATOM 15 CZ2 TRP 1 5.522 -0.301 -2.250 1.00 0.95 TRYP ATOM 16 HZ2 TRP 1 6.609 -1.715 -2.204 1.00 0.81 TRYP ATOM 17 CZ3 TRP 1 3.739 -1.549 -2.466 1.00 2.56 TRYP ATOM 18 HZ3 TRP 1 3.214 0.614 -4.111 1.00 1.78 TRYP ATOM 19 CH2 TRP 1 3.841 -1.525 -2.946 1.00 2.42 TRYP ATOM 20 HH2 TRP 1 3.484 0.561 -4.269 1.00 3.48 TRYP ATOM 21 C TRP 1 1.410 0.346 -0.738 1.00 2.46 TRYP ATOM 22 OT1 TRP 1 2.607 -0.727 0.015 1.00 4.51 TRYP ATOM 23 OT2 TRP 1 1.514 -0.885 0.403 1.00 4.02 TRYP ATOM 24 N TRP 1 1.278 1.272 -1.777 1.00 1.43 TRYP ATOM 25 HT1 TRP 1 1.797 2.539 -1.924 1.00 3.38 TRYP ATOM 26 HT2 TRP 1 0.948 1.454 -1.016 1.00 1.22 TRYP ATOM 27 HT3 TRP 1 1.786 3.195 -0.172 1.00 3.79 TRYP END X-PLOR> 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>{* =============================================================== *} X-PLOR>{* test 7: test no metrization *} X-PLOR>{* =============================================================== *} X-PLOR> X-PLOR>set seed=12345 end X-PLOR> X-PLOR>mmdg MMDG> verbose off MMDG> iacc=5. tacc=5. bacc=0.2 pacc=5. MMDG> ? --------------------------------------------------------------------------- REFErence=PARAmeter SHORtest-path-algorithm=AUTO BACCuracy=0.2000 TACCuracy=5.0000 PACCuracy=5.0000 IACCuracy=5.0000 Number of rigid groups= 0 Bound smoothing being used for 27 atoms. All atoms are embedded. DG-energy term: SCALe=1.0000 EXPOnent= 2 Number of selected atoms= 0 --------------------------------------------------------------------------- MMDG>end MMDG: no atoms will be metrized. DGSETNX: found 152 exclusions (1--2, 1--3) for repulsive lower bounds. DGNOMET: number of connections: 286 DGNOMET: using full matrix bound smoothing algorithm. X-PLOR> X-PLOR>set display=OUTPUT end X-PLOR>display $embedded TRUE X-PLOR>display $non_met_gap 3.42527 X-PLOR>display $dgscale 0.886231 X-PLOR> X-PLOR>vector do (x = x * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (y = y * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (z = z * $dgscale) (all) SELRPN: 27 atoms have been selected out of 27 X-PLOR> X-PLOR>energy end %atoms "TRYP-1 -TRP -HE3 " and "TRYP-1 -TRP -CZ2 " only 0.83 A apart --------------- cycle= 16 -------------------------------------------------- | Etotal =286.163 grad(E)=14.907 E(BOND)=80.284 E(ANGL)=15.395 | | E(DIHE)=0.000 E(IMPR)=34.907 E(VDW )=25.221 E(ELEC)=0.000 | | E(CDIH)=0.000 E(NOE )=130.356 | ------------------------------------------------------------------------------- X-PLOR>evaluate ($chi_ener=$impr) EVALUATE: symbol $CHI_ENER set to 34.9068 (real) X-PLOR>vector do (z=-z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>energy end %atoms "TRYP-1 -TRP -HE3 " and "TRYP-1 -TRP -CZ2 " only 0.83 A apart --------------- cycle= 17 -------------------------------------------------- | Etotal =285.884 grad(E)=14.904 E(BOND)=80.284 E(ANGL)=15.395 | | E(DIHE)=0.000 E(IMPR)=34.628 E(VDW )=25.221 E(ELEC)=0.000 | | E(CDIH)=0.000 E(NOE )=130.356 | ------------------------------------------------------------------------------- X-PLOR>if ($impr > $chi_ener) then NEXTCD: condition evaluated as false X-PLOR> vector do (z=-z) ( all ) X-PLOR>end if X-PLOR> X-PLOR>set message=off end coor fit end set message=on end R.m.s. diff. between fitted set and comp. set for selected atoms = 2.3824 X-PLOR>coor rms end COOR: ATTENTION: atom rms differences copied to RMSD array. COOR: rms= 2.382351, square sum= 153.2411, denominator= 27.0000 X-PLOR>vector do (b=rmsd ) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>write coords end REMARK FILENAME="stdout" REMARK file parallhdg.pro REMARK NOTE: these parameters are DEPRECATED. Please instead use protein.par. REMARK geometric energy function parameters for distance geometry and REMARK simulated annealing. REMARK DATE:24-Jan-08 16:50:15 created by user: schwitrs ATOM 1 CA TRP 1 1.122 0.812 -2.004 1.00 2.15 TRYP ATOM 2 HA TRP 1 1.400 1.874 -1.743 1.00 2.99 TRYP ATOM 3 CB TRP 1 2.434 0.510 -1.583 1.00 1.96 TRYP ATOM 4 HB1 TRP 1 2.234 0.927 -0.897 1.00 1.71 TRYP ATOM 5 HB2 TRP 1 1.817 0.176 -0.840 1.00 3.06 TRYP ATOM 6 CG TRP 1 3.548 0.630 -1.323 1.00 0.92 TRYP ATOM 7 CD1 TRP 1 3.924 -0.226 -0.649 1.00 1.65 TRYP ATOM 8 HD1 TRP 1 4.230 1.623 -0.380 1.00 1.86 TRYP ATOM 9 CD2 TRP 1 4.154 -0.856 -1.372 1.00 1.62 TRYP ATOM 10 NE1 TRP 1 4.846 -0.372 -0.035 1.00 1.04 TRYP ATOM 11 HE1 TRP 1 5.721 0.010 0.894 1.00 1.06 TRYP ATOM 12 CE2 TRP 1 4.930 -0.265 -0.760 1.00 1.10 TRYP ATOM 13 CE3 TRP 1 5.408 -0.453 -2.152 1.00 2.16 TRYP ATOM 14 HE3 TRP 1 4.181 0.178 -2.593 1.00 1.81 TRYP ATOM 15 CZ2 TRP 1 4.908 0.583 -2.587 1.00 1.89 TRYP ATOM 16 HZ2 TRP 1 6.710 2.131 -1.829 1.00 3.41 TRYP ATOM 17 CZ3 TRP 1 5.996 2.013 -2.957 1.00 2.75 TRYP ATOM 18 HZ3 TRP 1 5.269 -2.370 -4.529 1.00 2.64 TRYP ATOM 19 CH2 TRP 1 5.707 2.929 -3.784 1.00 3.62 TRYP ATOM 20 HH2 TRP 1 4.661 -1.424 -5.711 1.00 2.08 TRYP ATOM 21 C TRP 1 1.185 0.278 -0.869 1.00 2.47 TRYP ATOM 22 OT1 TRP 1 3.156 2.931 0.898 1.00 4.12 TRYP ATOM 23 OT2 TRP 1 2.156 4.420 1.619 1.00 2.75 TRYP ATOM 24 N TRP 1 0.852 2.252 -1.552 1.00 2.16 TRYP ATOM 25 HT1 TRP 1 0.506 -1.466 -0.898 1.00 1.34 TRYP ATOM 26 HT2 TRP 1 -0.531 2.466 -1.138 1.00 2.58 TRYP ATOM 27 HT3 TRP 1 0.129 -0.792 2.580 1.00 3.40 TRYP END X-PLOR> 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>{* =============================================================== *} X-PLOR>{* test 8: test pseudoatom correction *} X-PLOR>{* =============================================================== *} X-PLOR> X-PLOR>vector do (refx=x) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (refy=y) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR>vector do (refz=z) ( all ) SELRPN: 27 atoms have been selected out of 27 X-PLOR> X-PLOR>noe NOE> reset NOE> nres=100 NOE: allocating space for 100 restraints. NOE> assign ( name hb* ) ( name ca ) 4. 1. 2. SELRPN: 2 atoms have been selected out of 27 SELRPN: 1 atoms have been selected out of 27 NOE> assign ( name ca ) ( name hb* ) 7. 1. 2. SELRPN: 1 atoms have been selected out of 27 SELRPN: 2 atoms have been selected out of 27 NOE> assign ( name hb* ) ( name ht* ) 8. 1. 2. SELRPN: 2 atoms have been selected out of 27 SELRPN: 3 atoms have been selected out of 27 NOE>end X-PLOR> X-PLOR>flags exclude * include noe end X-PLOR> X-PLOR>mmdg MMDG> verbose=on MMDG> storebounds MMDG>end Pseudoatom correction applied to NOE # 1 Pseudoatom correction applied to atom pair "TRYP-1 -TRP -HB1 " "TRYP-1 -TRP -CA " distance range before correction: 6.0000 3.0000 distance range after correction: 6.8663 2.1337 Pseudoatom correction applied to atom pair "TRYP-1 -TRP -HB2 " "TRYP-1 -TRP -CA " distance range before correction: 6.0000 3.0000 distance range after correction: 6.8663 2.1337 Pseudoatom correction applied to NOE # 2 Pseudoatom correction applied to atom pair "TRYP-1 -TRP -CA " "TRYP-1 -TRP -HB1 " distance range before correction: 9.0000 6.0000 distance range after correction: 9.8663 5.1337 Pseudoatom correction applied to atom pair "TRYP-1 -TRP -CA " "TRYP-1 -TRP -HB2 " distance range before correction: 9.0000 6.0000 distance range after correction: 9.8663 5.1337 Pseudoatom correction applied to NOE # 3 Pseudoatom correction applied to atom pair "TRYP-1 -TRP -HB1 " "TRYP-1 -TRP -HT1 " distance range before correction: 10.0000 7.0000 distance range after correction: 11.8458 5.1542 Pseudoatom correction applied to atom pair "TRYP-1 -TRP -HB1 " "TRYP-1 -TRP -HT2 " distance range before correction: 10.0000 7.0000 distance range after correction: 11.8460 5.1540 Pseudoatom correction applied to atom pair "TRYP-1 -TRP -HB1 " "TRYP-1 -TRP -HT3 " distance range before correction: 10.0000 7.0000 distance range after correction: 11.8478 5.1522 Pseudoatom correction applied to atom pair "TRYP-1 -TRP -HB2 " "TRYP-1 -TRP -HT1 " distance range before correction: 10.0000 7.0000 distance range after correction: 11.8458 5.1542 Pseudoatom correction applied to atom pair "TRYP-1 -TRP -HB2 " "TRYP-1 -TRP -HT2 " distance range before correction: 10.0000 7.0000 distance range after correction: 11.8460 5.1540 Pseudoatom correction applied to atom pair "TRYP-1 -TRP -HB2 " "TRYP-1 -TRP -HT3 " distance range before correction: 10.0000 7.0000 distance range after correction: 11.8478 5.1522 finished initialization DGSMOOT: number of connections: 16 DGSMOOT: using sparse matrix bound smoothing algorithm. DGSMOOT: max. size of network (upper, lower): 4 4 MMDG: storing smoothed bounds matrix in memory. No metrization or embedding performed. X-PLOR> X-PLOR>stop HEAP: maximum use= 1532503 current use= 1181120 X-PLOR: total CPU time= 0.3200 s X-PLOR: entry time at 16:50:15 24-Jan-08 X-PLOR: exit time at 16:50:15 24-Jan-08