XPLOR-NIH version 2.9.5 C.D. Schwieters, J.J. Kuszewski, based on X-PLOR 3.851 by A.T. Brunger N. Tjandra, and G.M. Clore J. Magn. Res., 160, 66-74 (2003). http://nmr.cit.nih.gov/xplor-nih User: [unknown] on: x86/Linux at: 04-Jun-04 10:27:21 X-PLOR>remarks Asn MD with GB/HCT X-PLOR>remarks Tom Simonson, May, 2002. X-PLOR> X-PLOR> X-PLOR>!-------------------------------------------------------------- X-PLOR>! the initial time is the ONLY parameter that has to be changed X-PLOR>! $inittime is set to the last time of the previous run X-PLOR> X-PLOR>evaluate ($inittime = 0 {ps}) EVALUATE: symbol $INITTIME set to 0.00000 (real) X-PLOR>evaluate ($finaltime = $inittime + 100) {100 ps equilibration} EVALUATE: symbol $FINALTIME set to 100.000 (real) X-PLOR>set seed = 123456 end X-PLOR> X-PLOR> X-PLOR>topology RTFRDR> @TOPPAR:topamber.inp ASSFIL: file /home/schwitrs/xplor/toppar/topamber.inp opened. RTFRDR>REMARKS * AMBER Cornell et al. (parm94) force field conversion RTFRDR>REMARKS * See: JACS (1995) 117, 5179-5197. RTFRDR>REMARKS * nucleic acid part converted by tec3, march 1997 RTFRDR>REMARKS * protein part converted by tec3, february 1999 RTFRDR>REMARKS * RTFRDR>REMARKS 23 1 RTFRDR>REMARKS Converted to Xplor format, T. Simonson, July 2000. RTFRDR>REMARKS Nucleic acid part left out. RTFRDR> RTFRDR>set echo=false end RTFRDR> @TOPPAR:amberpatches.pro ASSFIL: file /home/schwitrs/xplor/toppar/amberpatches.pro opened. RTFRDR> REMARKS Amber topology for proteins RTFRDR> REMARKS FILENAME=patches.pro RTFRDR> RTFRDR> set echo=false end RTFRDR>end X-PLOR> X-PLOR>parameter @TOPPAR:paramber.gb.inp end ASSFIL: file /home/schwitrs/xplor/toppar/paramber.gb.inp opened. PARRDR>REMARKS * AMBER Cornell et al. (parm94) force field conversion PARRDR>REMARKS * See: JACS (1995) 117, 5179-5197. PARRDR>REMARKS * nucleic acid part converted by tec3, march 1997 PARRDR>REMARKS * protein part converted by tec3, feb 1999 PARRDR>REMARKS * PARRDR> PARRDR>set echo=false end PARRDR> PARRDR> PARRDR> PARRDR> PARRDR> PARRDR> PARRDR> PARRDR> end X-PLOR> X-PLOR> X-PLOR>segment SEGMENT>name="ASN1" SEGMENT>molecule name=ASN number=1 end SEGMENT>end SEGMNT: 1 residues were inserted into segment "ASN1" XPLOR: current counts (number in parenthesis is maximum) NATOM= 14(MAXA= 200) NBOND= 13(MAXB= 100) NTHETA= 20(MAXT= 100) NGRP= 1(MAXGRP= 100) NPHI= 28(MAXP= 100) NIMPHI= 2(MAXIMP= 100) NDON= 3(MAXPAD= 100) NACC= 2(MAXPAD= 100) NNB= 0(MAXNB= 0) X-PLOR>patch NASN refe=nil=(resid 1) end SELRPN: 14 atoms have been selected out of 14 MAPIC: Atom numbers being modified XPLOR: current counts (number in parenthesis is maximum) NATOM= 16(MAXA= 200) NBOND= 15(MAXB= 100) NTHETA= 19(MAXT= 100) NGRP= 1(MAXGRP= 100) NPHI= 25(MAXP= 100) NIMPHI= 2(MAXIMP= 100) NDON= 5(MAXPAD= 100) NACC= 2(MAXPAD= 100) NNB= 0(MAXNB= 0) X-PLOR>patch CASN refe=nil=(resid 1) end SELRPN: 16 atoms have been selected out of 16 %PATCH-ERR: atom HN not found MAPIC: Atom numbers being modified XPLOR: current counts (number in parenthesis is maximum) NATOM= 17(MAXA= 200) NBOND= 16(MAXB= 100) NTHETA= 18(MAXT= 100) NGRP= 1(MAXGRP= 100) NPHI= 22(MAXP= 100) NIMPHI= 3(MAXIMP= 100) NDON= 5(MAXPAD= 100) NACC= 3(MAXPAD= 100) NNB= 0(MAXNB= 0) X-PLOR> X-PLOR> X-PLOR>vector do (charge = charge + .2306) (name ht%) SELRPN: 3 atoms have been selected out of 17 X-PLOR>vector show sum (charge) (all) SELRPN: 17 atoms have been selected out of 17 VECTOR: sum over selected elements = 0.000000 X-PLOR> X-PLOR> X-PLOR> X-PLOR>segment SEGMENT>name="ASN1" SEGMENT>molecule name=ASN number=1 end %SEGMNT-ERR: attempt to enter duplicate residue ASN1 1 ASN SEGMENT>end SEGMNT: 1 residues were inserted into segment "ASN1" XPLOR: current counts (number in parenthesis is maximum) NATOM= 17(MAXA= 200) NBOND= 16(MAXB= 100) NTHETA= 18(MAXT= 100) NGRP= 1(MAXGRP= 100) NPHI= 22(MAXP= 100) NIMPHI= 3(MAXIMP= 100) NDON= 5(MAXPAD= 100) NACC= 3(MAXPAD= 100) NNB= 0(MAXNB= 0) X-PLOR>patch NTER refe="+"=(resid 1) end SELRPN: 17 atoms have been selected out of 17 XPLOR: current counts (number in parenthesis is maximum) NATOM= 17(MAXA= 200) NBOND= 16(MAXB= 100) NTHETA= 24(MAXT= 100) NGRP= 1(MAXGRP= 100) NPHI= 31(MAXP= 100) NIMPHI= 3(MAXIMP= 100) NDON= 5(MAXPAD= 100) NACC= 3(MAXPAD= 100) NNB= 0(MAXNB= 0) X-PLOR>patch CTER refe="-"=(resid 1) end SELRPN: 17 atoms have been selected out of 17 XPLOR: current counts (number in parenthesis is maximum) NATOM= 17(MAXA= 200) NBOND= 16(MAXB= 100) NTHETA= 27(MAXT= 100) NGRP= 1(MAXGRP= 100) NPHI= 37(MAXP= 100) NIMPHI= 3(MAXIMP= 100) NDON= 5(MAXPAD= 100) NACC= 3(MAXPAD= 100) NNB= 0(MAXNB= 0) X-PLOR> X-PLOR>vector show sum (charge) (all) SELRPN: 17 atoms have been selected out of 17 VECTOR: sum over selected elements = 0.000000 X-PLOR> X-PLOR> X-PLOR> X-PLOR>parameter PARRDR>nbonds NBDSET> atom cdie trunc NBDSET> e14fac=0.8333333 ! use this to reproduce amber elec NBDSET> cutnb 500. ctonnb 480. ctofnb 490. ! essentially no cutoff NBDSET> tolerance=100. ! only build the nonbonded list once NBDSET> nbxmod 5 vswitch NBDSET> wmin=1.0 NBDSET>end %NBDSET-ERR: inconsistent CUTNB, TOLErance, CTOFNB given. Reset. PARRDR>end X-PLOR> X-PLOR>parameters nbonds NBDSET> EPS=1. WEPS=80. offset=0.09 GBHCT ! GB parameters NBDSET>end PARRDR>end X-PLOR> X-PLOR> X-PLOR> X-PLOR> X-PLOR>! gauche minus conformer X-PLOR>coor ! @data/asn.-80.10.pdb COOR>REMARK CHI1=-80, CHI2=10; ENERGY = -3.92838 COOR>REMARK DATE: 3/ 6/98 14:38:33 CREATED BY USER: simonson COOR>ATOM 1 N ASN 1 26.522 -15.164 -2.651 0.00 0.00 ASN1 COOR>ATOM 2 HT1 ASN 1 25.821 -14.402 -2.738 0.00 0.00 ASN1 X-PLOR> X-PLOR>write coor output=asn.-80.10.pdb end ASSFIL: file asn.-80.10.pdb opened. X-PLOR> X-PLOR> X-PLOR>@TOPPAR:volumes.amber ASSFIL: file /home/schwitrs/xplor/toppar/volumes.amber opened. X-PLOR>vector do (rmsd = 0.0000 ) (chem H ) SELRPN: 5 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 2.1447 ) (chem HO ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 2.1447 ) (chem HS ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 0.0000 ) (chem HC ) SELRPN: 2 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 0.0000 ) (chem H1 ) SELRPN: 1 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 9.2028 ) (chem H2 ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 9.2028 ) (chem H3 ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 9.2028 ) (chem HP ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 9.2028 ) (chem HA ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 9.2028 ) (chem H4 ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 9.2028 ) (chem H5 ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 2.1447 ) (chem HW ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 14.0915 ) (chem O ) SELRPN: 1 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 13.9816 ) (chem O2 ) SELRPN: 2 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 14.1372 ) (chem OW ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 14.1372 ) (chem OH ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 14.1372 ) (chem OS ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 13.7205 ) (chem CT ) SELRPN: 2 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 20.5796 ) (chem CA ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 12.5567 ) (chem C ) SELRPN: 2 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 20.5796 ) (chem CM ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 20.5796 ) (chem CS ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 20.5796 ) (chem CB ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 20.5796 ) (chem CC ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 20.5796 ) (chem CN ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 20.5796 ) (chem CK ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 20.5796 ) (chem CQ ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 20.5796 ) (chem CW ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 20.5796 ) (chem CV ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 20.5796 ) (chem CR ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 20.5796 ) (chem CX ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 20.5796 ) (chem CY ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 20.5796 ) (chem CD ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 15.5986 ) (chem N* ) SELRPN: 2 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 20.5147 ) (chem N ) SELRPN: 2 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 15.5986 ) (chem N2 ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 15.5986 ) (chem N3 ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 15.5986 ) (chem NA ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 15.5986 ) (chem NB ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 24.4291 ) (chem S ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 24.4291 ) (chem SH ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 1.8500 ) (chem P ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 1.0000 ) (chem IM ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 1.0000 ) (chem LI ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 1.0000 ) (chem IP ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 1.0000 ) (chem K ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 1.0000 ) (chem RB ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 1.0000 ) (chem I ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 1.4700 ) (chem F ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = 1.0000 ) (chem IB ) SELRPN: 0 atoms have been selected out of 17 X-PLOR>vector do (rmsd = rmsd * 0.9) (all) ! reduce volumes by 10% SELRPN: 17 atoms have been selected out of 17 X-PLOR>flags include gbse gbin end X-PLOR>parameter reduce selection=(all) overwrite=true mode=average end end SELRPN: 17 atoms have been selected out of 17 REDUCE: creating 16 new dihedral parameters REDUCE: creating 3 new improper parameters X-PLOR> X-PLOR>energy end BSOLVINI: BSOLVMAX = 6.15472926300969 MAKINB: mode 5 found 77 exclusions, 34 interactions(1-4) and 43 GB exclusions --------------- cycle= 1 -------------------------------------------------- | Etotal =-211.753 grad(E)=13.951 E(BOND)=3.252 E(ANGL)=6.259 | | E(DIHE)=4.875 E(IMPR)=0.003 E(VDW )=1.021 E(ELEC)=-118.620 | | E(GBSE)=-501.255 E(GBIN)=392.713 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR> X-PLOR>!----------------------------- X-PLOR>! shake TIP3p's and ALL bonds X-PLOR>!shake X-PLOR>! ncon=6000 X-PLOR>! reference=parameter bonds ( not resname TIP3 ) ( all ) X-PLOR>! tolerance=1.0e-08 X-PLOR>!end X-PLOR> X-PLOR> X-PLOR>! weakly restrain Calpha position X-PLOR>vector do (harmonic = 0.5) (name ca) SELRPN: 1 atoms have been selected out of 17 X-PLOR>coor disp=reference @asn.-80.10.pdb COOR: coordinates read into REFE set ASSFIL: file asn.-80.10.pdb opened. COOR>REMARK FILENAME="asn.-80.10.pdb" COOR>REMARK CHI1=-80, CHI2=10; ENERGY = -3.92838 COOR>REMARK DATE:04-Jun-04 10:27:22 created by user: [unknown] COOR>ATOM 1 N ASN 1 26.522 -15.164 -2.651 0.00 0.00 ASN1 COOR>ATOM 2 OT1 ASN 1 23.884 -16.213 -0.858 0.00 0.00 ASN1 X-PLOR>constraints harmonic end Obsolete syntax: please use REStraints HARMonic X-PLOR>flags include harmonic end X-PLOR> X-PLOR> X-PLOR> X-PLOR>!----------------- X-PLOR>! Now run dynamics X-PLOR> X-PLOR> X-PLOR>!------------------------------------------ X-PLOR>! $time is set to last time of previous run X-PLOR> X-PLOR>evaluate ($time = $inittime) EVALUATE: symbol $TIME set to 0.00000 (real) X-PLOR> X-PLOR> X-PLOR>!--------------------------------------------------------------- X-PLOR>! first, read "restart" files or initial coords and assign velos X-PLOR> X-PLOR> X-PLOR> X-PLOR>if ($time > 0) then NEXTCD: condition evaluated as false X-PLOR> X-PLOR> coor disp=main @@$fincrd X-PLOR> coor disp=comp @@$finvel X-PLOR> X-PLOR> vector do (vx = xcomp) (attribute xcomp < 999.0) X-PLOR> vector do (vy = ycomp) (attribute xcomp < 999.0) X-PLOR> vector do (vz = zcomp) (attribute xcomp < 999.0) X-PLOR> vector do (vx = maxwell(250)) (attribute xcomp > 999.) X-PLOR> vector do (vy = maxwell(250)) (attribute xcomp > 999.) X-PLOR> vector do (vz = maxwell(250)) (attribute xcomp > 999.) X-PLOR> X-PLOR>else X-PLOR> X-PLOR> X-PLOR> vector do (vx = maxwell(250)) (all) SELRPN: 17 atoms have been selected out of 17 X-PLOR> vector do (vy = maxwell(250)) (all) SELRPN: 17 atoms have been selected out of 17 X-PLOR> vector do (vz = maxwell(250)) (all) SELRPN: 17 atoms have been selected out of 17 X-PLOR> X-PLOR>end if X-PLOR> X-PLOR> X-PLOR> X-PLOR>!------------------------------------- X-PLOR>! relax initial bad contacts X-PLOR>if ($time = 0.) then NEXTCD: condition evaluated as true X-PLOR>minimize powell nstep=10 drop=10 end POWELL: number of degrees of freedom= 51 BSOLVINI: BSOLVMAX = 6.15472926300969 --------------- cycle= 1 ------ stepsize= 0.0000 ----------------------- | Etotal =-211.753 grad(E)=13.951 E(BOND)=3.252 E(ANGL)=6.259 | | E(DIHE)=4.875 E(IMPR)=0.003 E(VDW )=1.021 E(ELEC)=-118.620 | | E(HARM)=0.000 E(GBSE)=-501.255 E(GBIN)=392.713 | ------------------------------------------------------------------------------- --------------- cycle= 2 ------ stepsize= 0.0014 ----------------------- | Etotal =-203.245 grad(E)=37.225 E(BOND)=13.811 E(ANGL)=8.344 | | E(DIHE)=4.880 E(IMPR)=0.004 E(VDW )=0.863 E(ELEC)=-121.395 | | E(HARM)=0.000 E(GBSE)=-499.484 E(GBIN)=389.732 | ------------------------------------------------------------------------------- --------------- cycle= 3 ------ stepsize= 0.0004 ----------------------- | Etotal =-213.931 grad(E)=6.300 E(BOND)=2.321 E(ANGL)=6.271 | | E(DIHE)=4.875 E(IMPR)=0.000 E(VDW )=0.961 E(ELEC)=-119.485 | | E(HARM)=0.000 E(GBSE)=-500.693 E(GBIN)=391.819 | ------------------------------------------------------------------------------- --------------- cycle= 4 ------ stepsize= 0.0004 ----------------------- | Etotal =-214.602 grad(E)=3.954 E(BOND)=1.700 E(ANGL)=6.288 | | E(DIHE)=4.870 E(IMPR)=0.000 E(VDW )=0.931 E(ELEC)=-119.687 | | E(HARM)=0.000 E(GBSE)=-500.192 E(GBIN)=391.488 | ------------------------------------------------------------------------------- --------------- cycle= 5 ------ stepsize= 0.0005 ----------------------- | Etotal =-214.841 grad(E)=4.691 E(BOND)=1.429 E(ANGL)=6.382 | | E(DIHE)=4.866 E(IMPR)=0.001 E(VDW )=0.902 E(ELEC)=-119.903 | | E(HARM)=0.000 E(GBSE)=-499.655 E(GBIN)=391.138 | ------------------------------------------------------------------------------- --------------- cycle= 6 ------ stepsize= 0.0009 ----------------------- | Etotal =-215.459 grad(E)=2.894 E(BOND)=0.944 E(ANGL)=6.776 | | E(DIHE)=4.858 E(IMPR)=0.003 E(VDW )=0.826 E(ELEC)=-120.073 | | E(HARM)=0.000 E(GBSE)=-499.042 E(GBIN)=390.250 | ------------------------------------------------------------------------------- --------------- cycle= 7 ------ stepsize= 0.0003 ----------------------- | Etotal =-215.491 grad(E)=3.509 E(BOND)=0.889 E(ANGL)=6.951 | | E(DIHE)=4.856 E(IMPR)=0.003 E(VDW )=0.805 E(ELEC)=-120.124 | | E(HARM)=0.000 E(GBSE)=-498.864 E(GBIN)=389.993 | ------------------------------------------------------------------------------- --------------- cycle= 8 ------ stepsize= 0.0012 ----------------------- | Etotal =-215.604 grad(E)=5.326 E(BOND)=1.283 E(ANGL)=7.224 | | E(DIHE)=4.835 E(IMPR)=0.007 E(VDW )=0.739 E(ELEC)=-120.204 | | E(HARM)=0.000 E(GBSE)=-499.061 E(GBIN)=389.572 | ------------------------------------------------------------------------------- --------------- cycle= 9 ------ stepsize= -0.0005 ----------------------- | Etotal =-215.706 grad(E)=2.807 E(BOND)=1.006 E(ANGL)=7.080 | | E(DIHE)=4.843 E(IMPR)=0.005 E(VDW )=0.765 E(ELEC)=-120.169 | | E(HARM)=0.000 E(GBSE)=-498.982 E(GBIN)=389.745 | ------------------------------------------------------------------------------- --------------- cycle= 10 ------ stepsize= 0.0007 ----------------------- | Etotal =-215.904 grad(E)=2.196 E(BOND)=1.183 E(ANGL)=7.145 | | E(DIHE)=4.838 E(IMPR)=0.007 E(VDW )=0.676 E(ELEC)=-120.367 | | E(HARM)=0.000 E(GBSE)=-499.379 E(GBIN)=389.994 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR>minimize powell nstep=10 drop=10 end POWELL: number of degrees of freedom= 51 --------------- cycle= 1 ------ stepsize= 0.0000 ----------------------- | Etotal =-215.904 grad(E)=2.196 E(BOND)=1.183 E(ANGL)=7.145 | | E(DIHE)=4.838 E(IMPR)=0.007 E(VDW )=0.676 E(ELEC)=-120.367 | | E(HARM)=0.000 E(GBSE)=-499.379 E(GBIN)=389.994 | ------------------------------------------------------------------------------- --------------- cycle= 2 ------ stepsize= 0.0407 ----------------------- | Etotal =44.013 grad(E)=153.080 E(BOND)=226.985 E(ANGL)=44.373 | | E(DIHE)=4.973 E(IMPR)=0.411 E(VDW )=-0.994 E(ELEC)=-119.523 | | E(HARM)=0.000 E(GBSE)=-508.543 E(GBIN)=396.331 | ------------------------------------------------------------------------------- --------------- cycle= 3 ------ stepsize= 0.0008 ----------------------- | Etotal =-215.999 grad(E)=1.774 E(BOND)=1.173 E(ANGL)=7.121 | | E(DIHE)=4.836 E(IMPR)=0.005 E(VDW )=0.614 E(ELEC)=-120.362 | | E(HARM)=0.000 E(GBSE)=-499.545 E(GBIN)=390.159 | ------------------------------------------------------------------------------- --------------- cycle= 4 ------ stepsize= 0.0008 ----------------------- | Etotal =-216.086 grad(E)=1.230 E(BOND)=1.262 E(ANGL)=7.040 | | E(DIHE)=4.833 E(IMPR)=0.004 E(VDW )=0.563 E(ELEC)=-120.353 | | E(HARM)=0.000 E(GBSE)=-499.866 E(GBIN)=390.432 | ------------------------------------------------------------------------------- --------------- cycle= 5 ------ stepsize= 0.0005 ----------------------- | Etotal =-216.103 grad(E)=1.696 E(BOND)=1.347 E(ANGL)=7.002 | | E(DIHE)=4.830 E(IMPR)=0.004 E(VDW )=0.528 E(ELEC)=-120.348 | | E(HARM)=0.000 E(GBSE)=-500.087 E(GBIN)=390.620 | ------------------------------------------------------------------------------- --------------- cycle= 6 ------ stepsize= 0.0013 ----------------------- | Etotal =-216.140 grad(E)=2.474 E(BOND)=1.659 E(ANGL)=7.126 | | E(DIHE)=4.816 E(IMPR)=0.004 E(VDW )=0.443 E(ELEC)=-120.122 | | E(HARM)=0.000 E(GBSE)=-500.617 E(GBIN)=390.550 | ------------------------------------------------------------------------------- --------------- cycle= 7 ------ stepsize= -0.0005 ----------------------- | Etotal =-216.162 grad(E)=1.405 E(BOND)=1.513 E(ANGL)=7.073 | | E(DIHE)=4.821 E(IMPR)=0.004 E(VDW )=0.475 E(ELEC)=-120.207 | | E(HARM)=0.000 E(GBSE)=-500.418 E(GBIN)=390.577 | ------------------------------------------------------------------------------- --------------- cycle= 8 ------ stepsize= 0.0008 ----------------------- | Etotal =-216.209 grad(E)=1.196 E(BOND)=1.503 E(ANGL)=7.247 | | E(DIHE)=4.817 E(IMPR)=0.004 E(VDW )=0.426 E(ELEC)=-120.143 | | E(HARM)=0.000 E(GBSE)=-500.531 E(GBIN)=390.468 | ------------------------------------------------------------------------------- --------------- cycle= 9 ------ stepsize= 0.0002 ----------------------- | Etotal =-216.211 grad(E)=1.425 E(BOND)=1.508 E(ANGL)=7.287 | | E(DIHE)=4.816 E(IMPR)=0.003 E(VDW )=0.415 E(ELEC)=-120.129 | | E(HARM)=0.000 E(GBSE)=-500.556 E(GBIN)=390.444 | ------------------------------------------------------------------------------- --------------- cycle= 10 ------ stepsize= 0.0009 ----------------------- | Etotal =-216.273 grad(E)=1.011 E(BOND)=1.460 E(ANGL)=7.498 | | E(DIHE)=4.808 E(IMPR)=0.003 E(VDW )=0.362 E(ELEC)=-120.114 | | E(HARM)=0.000 E(GBSE)=-500.509 E(GBIN)=390.219 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR>end if X-PLOR> X-PLOR> X-PLOR> X-PLOR>!-------------------------- X-PLOR>! generate output filenames X-PLOR> X-PLOR>!evaluate ($traj = "output/dyn" + encode($time) + ".crd") X-PLOR>!evaluate ($velo= "output/dyn" + encode($time) + ".vel") X-PLOR>!evaluate ($restart ="output/dyn"+encode($time) + ".rst") X-PLOR> X-PLOR> X-PLOR>!-------------- X-PLOR>! let it go X-PLOR> X-PLOR>display CPU= $CPU sec. CPU= 0.22 sec. X-PLOR> X-PLOR> X-PLOR>dynamics verlet DYNAmics> nstep=50 timest=0.001 {ps} ! 100 ps dynamics DYNAmics> iasvel=current ! current velocities DYNAmics> nprint=25 iprfrq=250 ! statistics output DYNAmics> ascii=true DYNAmics> !traj=$traj ! coord trajectory DYNAmics> nsavc=250 DYNAmics> vascii=true voffset=800 DYNAmics> !velo=$velo ! velocity trajectory DYNAmics> nsavv=10000 DYNAmics> !save=$restart DYNAmics> isvfrq=100000 ! restart file DYNAmics>end DYNAMC: number of degrees of freedom= 51 ASSVEL: current velocities taken. CENMAS: Information about center of free masses position [A] : 26.24970 -16.95761 -2.21097 velocity [A/ps] : 0.99097 0.93458 0.72651 ang. mom. [amu A/ps] : 107.36882 195.61338 -185.40572 kin. ener. [Kcal/mol] : 0.37634 ROTSTP: CM translation and rotation removed. CENMAS: Information about center of free masses position [A] : 26.24970 -16.95761 -2.21097 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 --------------- 2-step Verlet initialization ---------------------------------- | E(kin)+E(total)=-204.190 E(kin)=12.083 temperature=238.449 | | Etotal =-216.273 grad(E)=1.011 E(BOND)=1.460 E(ANGL)=7.498 | | E(DIHE)=4.808 E(IMPR)=0.003 E(VDW )=0.362 E(ELEC)=-120.114 | | E(HARM)=0.000 E(GBSE)=-500.509 E(GBIN)=390.219 | ------------------------------------------------------------------------------- --------------- step= 25 at 0.02500 ps -------------------------------- | E(kin)+E(total)=-204.066 E(kin)=6.968 temperature=137.515 | | Etotal =-211.035 grad(E)=11.572 E(BOND)=3.000 E(ANGL)=11.203 | | E(DIHE)=5.191 E(IMPR)=0.412 E(VDW )=0.437 E(ELEC)=-123.385 | | E(HARM)=0.000 E(GBSE)=-499.650 E(GBIN)=391.757 | ------------------------------------------------------------------------------- --------------- step= 50 at 0.05000 ps -------------------------------- | E(kin)+E(total)=-204.061 E(kin)=5.779 temperature=114.038 | | Etotal =-209.839 grad(E)=13.119 E(BOND)=3.417 E(ANGL)=12.139 | | E(DIHE)=5.262 E(IMPR)=0.605 E(VDW )=0.528 E(ELEC)=-123.038 | | E(HARM)=0.000 E(GBSE)=-498.118 E(GBIN)=389.365 | ------------------------------------------------------------------------------- CENMAS: Information about center of free masses position [A] : 26.24970 -16.95761 -2.21097 velocity [A/ps] : 0.00000 0.00000 0.00000 ang. mom. [amu A/ps] : 0.00000 0.00000 0.00000 kin. ener. [Kcal/mol] : 0.00000 DCNTRL: current coordinates in X, Y, Z DCNTRL: current velocities in VX, VY, VZ X-PLOR> X-PLOR> X-PLOR> X-PLOR> X-PLOR>stop HEAP: maximum use= 957915 current use= 917203 X-PLOR: total CPU time= 0.2400 s X-PLOR: entry time at 10:27:21 04-Jun-04 X-PLOR: exit time at 10:27:22 04-Jun-04