X-PLOR: V3.828 user: xplor on: HP-UX at: 11-Feb-96 13: 6:31 Author: Axel T. Brunger Copyright: 1988-95 (Yale University), 1987 (Harvard University) X-PLOR> remarks file generate/generatemetal.inp X-PLOR> remarks Sample: generate protein structure with metal cluster X-PLOR> X-PLOR> topology RTFRDR> @TOPPAR:tophcsdx.pro ASSFIL: file /Net/franklin/u6/xplor/xplor_hp/toppar/tophcsdx.pro opened. RTFRDR>remarks file TOPPAR/tophcsdx_new.pro (5/26/92) RTFRDR>REMARKS TOPHCSDx.PRO: Original XPLOR toph19x.pro modified according to RTFRDR>REMARKS R. A. Engh and R. Huber, Acta Cryst, Sect A, 1991) RTFRDR>REMARKS with additional atom types. RTFRDR>REMARKS =============================== RTFRDR>REMARKS Charges and atom order modified for neutral GROUPs. RTFRDR>REMARKS Histidine charges set to Del Bene and Cohen sto-3g calculations. RTFRDR>REMARKS Amide charges set to match the experimental dipole moment. RTFRDR>REMARKS Default for HIStidines is the doubly protonated state RTFRDR> RTFRDR>set echo=false end RTFRDR>set echo=true end RTFRDR> RTFRDR> {*Append the metal cluster*} RTFRDR> autogenerate angles=true end {*topology. *} RTFRDR> RTFRDR> mass SC 32.0600 RTFRDR> mass FE 55.847 RTFRDR> RTFRDR> RTFRDR> RESIdue FS4 {*Generate the cluster itself. *} RESIDUE> {*The name FS4 has to match what*} RESIDUE> {*you are using for the residue *} RESIDUE> GROUP {*name in the coordinate file. *} RESIDUE> ATOM FE1 type FE charge 2.5 end RESIDUE> ATOM FE2 type FE charge 2.5 end RESIDUE> ATOM FE3 type FE charge 2.5 end RESIDUE> ATOM FE4 type FE charge 2.5 end RESIDUE> ATOM S1 type SC charge -2.0 end RESIDUE> ATOM S2 type SC charge -2.0 end RESIDUE> ATOM S3 type SC charge -2.0 end RESIDUE> ATOM S4 type SC charge -2.0 end RESIDUE> RESIDUE> bond FE1 S1 bond FE1 S2 bond FE1 S3 {*These are connectivities.*} RESIDUE> bond FE2 S1 bond FE2 S2 bond FE2 S4 RESIDUE> bond FE3 S1 bond FE3 S3 bond FE3 S4 RESIDUE> bond FE4 S2 bond FE4 S3 bond FE4 S4 RESIDUE> RESIDUE> END RTFRDR> {*Generate the patch topology,*} RTFRDR> {*which will be used in the *} RTFRDR> PREsidue PFS4 {*PATCh command. *} RESIDUE> GROUp RESIDUE> MODIfy ATOM 1CB CHARge=0.00 END RESIDUE> MODIfy ATOM 1SG TYPE=SC CHARge=-1.00 END RESIDUE> GROUp RESIDUE> MODIfy ATOM 2CB CHARge=0.00 END RESIDUE> MODIfy ATOM 2SG TYPE=SC CHARge=-1.00 END RESIDUE> GROUp RESIDUE> MODIfy ATOM 3CB CHARge=0.00 END RESIDUE> MODIfy ATOM 3SG TYPE=SC CHARge=-1.00 END RESIDUE> GROUp RESIDUE> MODIfy ATOM 4CB CHARge=0.00 END RESIDUE> MODIfy ATOM 4SG TYPE=SC CHARge=-1.00 END RESIDUE> RESIDUE> ADD BOND 5FE1 1SG {*These are the covalent bonds*} RESIDUE> ADD BOND 5FE2 2SG {*between the CYSs and the *} RESIDUE> ADD BOND 5FE3 3SG {*cluster. *} RESIDUE> ADD BOND 5FE4 4SG RESIDUE> RESIDUE> {*Autogenerate does not work yet*} RESIDUE> {*for patch residues. *} RESIDUE> RESIDUE> ADD ANGLe 1CB 1SG 5FE1 ADD ANGLe 2CB 2SG 5FE2 RESIDUE> ADD ANGLe 3CB 3SG 5FE3 ADD ANGLe 4CB 4SG 5FE4 RESIDUE> RESIDUE> ADD ANGLe 1SG 5FE1 5S2 ADD ANGLe 1SG 5FE1 5S1 RESIDUE> ADD ANGLe 1SG 5FE1 5S3 RESIDUE> RESIDUE> ADD ANGLe 2SG 5FE2 5S2 ADD ANGLe 2SG 5FE2 5S1 RESIDUE> ADD ANGLe 2SG 5FE2 5S4 RESIDUE> RESIDUE> ADD ANGLe 3SG 5FE3 5S3 ADD ANGLe 3SG 5FE3 5S1 RESIDUE> ADD ANGLe 3SG 5FE3 5S4 RESIDUE> RESIDUE> ADD ANGLe 4SG 5FE4 5S2 ADD ANGLe 4SG 5FE4 5S3 RESIDUE> ADD ANGLe 4SG 5FE4 5S4 RESIDUE> END RTFRDR> end X-PLOR> X-PLOR> parameter PARRDR> PARRDR> @TOPPAR:parhcsdx.pro ASSFIL: file /Net/franklin/u6/xplor/xplor_hp/toppar/parhcsdx.pro opened. PARRDR>REMARK Parameter file including bond and angle parameters PARRDR>REMARK derived from Cambridge Data Base model structures PARRDR>REMARK (R. A. Engh and R. Huber, Acta Cryst. Sect. A., 1991). PARRDR>REMARK Dihedral, improper, and non-bonded parameters taken PARRDR>REMARK from param19x (XPLOR--Axel T. Brunger, Yale University, PARRDR>REMARK BRUNGER@YALEVMS) and assigned to new atom types PARRDR>REMARK where appropriate. PARRDR> PARRDR>set echo=false end PARRDR> {*Append parameters for metal*} PARRDR> bonds SC FE 1000.0 2.33 {*cluster. *} PARRDR> bonds FE FE 1000.0 2.75 PARRDR> bonds SC SC 1000.0 3.60 PARRDR> bonds CH2E SC 1000.0 1.81 PARRDR> PARRDR> PARRDR> angle SC FE SC 500.0 112.0 PARRDR> angle FE SC FE 500.0 75.0 PARRDR> angle FE SC CH2E 500.0 109.5 PARRDR> angle CH1E CH2E SC 500.0 114.400 PARRDR> PARRDR> PARRDR> ! eps sigma eps(1:4) sigma(1:4) PARRDR> ! (kcal/mol) (A) PARRDR> ! --------------------------------------- PARRDR> nonbonded FE 0.1 1.15 0.1 1.15 PARRDR> nonbonded SC 0.0430 3.3676 0.0430 3.3676 PARRDR> PARRDR> nbonds {*This statement specifies the*} NBDSET> atom cdie shift eps=1.0 e14fac=0.4 {*nonbonded interaction energy*} NBDSET> cutnb=7.5 ctonnb=6.0 ctofnb=6.5 {*options. Note the reduced *} NBDSET> nbxmod=5 vswitch {*nonbonding cutoff to save *} NBDSET> end {*CPU time. *} PARRDR> end X-PLOR> {*Split the coordinate file into*} X-PLOR> {*two files, one containing the *} X-PLOR> {*protein coordinates, the other*} X-PLOR> {*the metal cluster *} X-PLOR> {*coordinates. *} X-PLOR> X-PLOR> {*First, generate protein.*} X-PLOR> segment SEGMENT> name="2FXB" SEGMENT> chain CHAIN> @TOPPAR:toph19.pep ASSFIL: file /Net/franklin/u6/xplor/xplor_hp/toppar/toph19.pep opened. CHAIN>REMARKS TOPH19.pep -MACRO for protein sequence CHAIN>SET ECHO=FALSE END CHAIN> coordinates @test_2fxb_protein.pdb SEGMNT: sequence read from coordinate file ASSFIL: file test_2fxb_protein.pdb opened. COOR>REMARKS ELECTRON TRANSPORT 08-FEB-90 2FXB COOR>REMARKS FERREDOXIN COOR>REMARKS (BACILLUS THERMOPROTEOLYTICUS) COOR>REMARKS K.FUKUYAMA,T.TSUKIHARA,Y.KATSUBE COOR>REMARKS file: test_2fxb_protein.pdb COOR>ATOM 1 N PRO 1 13.946 -7.470 7.811 1.00 0.00 2FXB 78 MAPIC: Atom numbers being modified MAPIC: Atom numbers being modified CHAIN> end SEGMENT> end SEGMNT: 81 residues were inserted into segment "2FXB" XPLOR: current counts (number in parenthesis is maximum) NATOM= 716(MAXA= 24000) NBOND= 728(MAXB= 24000) NTHETA= 1048(MAXT= 40000) NGRP= 83(MAXGRP= 24000) NPHI= 416(MAXP= 50000) NIMPHI= 335(MAXIMP= 24000) NDON= 104(MAXPAD= 4000) NACC= 136(MAXPAD= 4000) NNB= 0(MAXNB= 3000) X-PLOR> coordinates @test_2fxb_protein.pdb ASSFIL: file test_2fxb_protein.pdb opened. COOR>REMARKS ELECTRON TRANSPORT 08-FEB-90 2FXB COOR>REMARKS FERREDOXIN COOR>REMARKS (BACILLUS THERMOPROTEOLYTICUS) COOR>REMARKS K.FUKUYAMA,T.TSUKIHARA,Y.KATSUBE COOR>REMARKS file: test_2fxb_protein.pdb COOR>ATOM 1 N PRO 1 13.946 -7.470 7.811 1.00 0.00 2FXB 78 COOR>ATOM 2 CA PRO 1 14.141 -7.568 6.363 1.00 0.00 2FXB 79 %READC-ERR: still 104 missing coordinates (in selected subset) X-PLOR> X-PLOR> {*Now generate metal cluster.*} X-PLOR> segment SEGMENT> name="2FXB" SEGMENT> chain CHAIN> coordinates @test_2fxb_metal.pdb SEGMNT: sequence read from coordinate file ASSFIL: file test_2fxb_metal.pdb opened. COOR>REMARKS ELECTRON TRANSPORT 08-FEB-90 2FXB COOR>REMARKS FERREDOXIN COOR>REMARKS (BACILLUS THERMOPROTEOLYTICUS) COOR>REMARKS K.FUKUYAMA,T.TSUKIHARA,Y.KATSUBE COOR>REMARKS file: test_2fxb_metal.pdb COOR>ATOM 614 FE1 FS4 82 9.162 9.801 12.218 1.00 0.00 2FXB 691 CHAIN> CHAIN> end SEGMENT> end SEGMNT: 1 residues were inserted into segment "2FXB" XPLOR: current counts (number in parenthesis is maximum) NATOM= 724(MAXA= 24000) NBOND= 740(MAXB= 24000) NTHETA= 1072(MAXT= 40000) NGRP= 84(MAXGRP= 24000) NPHI= 416(MAXP= 50000) NIMPHI= 335(MAXIMP= 24000) NDON= 104(MAXPAD= 4000) NACC= 136(MAXPAD= 4000) NNB= 0(MAXNB= 3000) X-PLOR> coordinates @test_2fxb_metal.pdb ASSFIL: file test_2fxb_metal.pdb opened. COOR>REMARKS ELECTRON TRANSPORT 08-FEB-90 2FXB COOR>REMARKS FERREDOXIN COOR>REMARKS (BACILLUS THERMOPROTEOLYTICUS) COOR>REMARKS K.FUKUYAMA,T.TSUKIHARA,Y.KATSUBE COOR>REMARKS file: test_2fxb_metal.pdb COOR>ATOM 614 FE1 FS4 82 9.162 9.801 12.218 1.00 0.00 2FXB 691 COOR>ATOM 615 FE2 FS4 82 11.656 10.815 11.800 1.00 0.00 2FXB 692 %READC-ERR: still 104 missing coordinates (in selected subset) X-PLOR> X-PLOR> {*Now generate the *} X-PLOR> {*covalent links between the*} X-PLOR> patch PFS4 {*cluster and the protein. *} PATCH> reference=1=( resid 11 ) SELRPN: 7 atoms have been selected out of 724 PATCH> reference=2=( resid 14 ) SELRPN: 7 atoms have been selected out of 724 PATCH> reference=3=( resid 17 ) SELRPN: 7 atoms have been selected out of 724 PATCH> reference=4=( resid 61 ) SELRPN: 7 atoms have been selected out of 724 PATCH> reference=5=( resid 82 ) SELRPN: 8 atoms have been selected out of 724 PATCH> end MAPIC: Atom numbers being modified XPLOR: current counts (number in parenthesis is maximum) NATOM= 724(MAXA= 24000) NBOND= 744(MAXB= 24000) NTHETA= 1088(MAXT= 40000) NGRP= 88(MAXGRP= 24000) NPHI= 416(MAXP= 50000) NIMPHI= 335(MAXIMP= 24000) NDON= 104(MAXPAD= 4000) NACC= 136(MAXPAD= 4000) NNB= 0(MAXNB= 3000) X-PLOR> X-PLOR> flags exclude vdw elec end {*Do hydrogen building w/o vdw*} X-PLOR> {*and elec. *} X-PLOR> hbuild {*This statement builds missing *} HBUILD> selection=( hydrogen ) {*hydrogens, which are needed for*} SELRPN: 104 atoms have been selected out of 724 HBUILD> phistep=45 {*the force field. *} HBUILD> end HBUILD: dihedral PHI STePs for spin = 45.0000 HBUILD: cutoff during water acceptor search = 7.5000 HBUILD: HT1 ,HT2 , placed for donor 2FXB 1 PRO N . HBUILD: H , , placed for donor 2FXB 2 LYS N . HBUILD: H , , placed for donor 2FXB 3 TYR N . HBUILD: H , , placed for donor 2FXB 4 THR N . HBUILD: H , , placed for donor 2FXB 5 ILE N . HBUILD: H , , placed for donor 2FXB 6 VAL N . HBUILD: H , , placed for donor 2FXB 7 ASP N . HBUILD: H , , placed for donor 2FXB 8 LYS N . HBUILD: H , , placed for donor 2FXB 9 GLU N . HBUILD: H , , placed for donor 2FXB 10 THR N . HBUILD: H , , placed for donor 2FXB 11 CYS N . HBUILD: H , , placed for donor 2FXB 12 ILE N . HBUILD: H , , placed for donor 2FXB 13 ALA N . HBUILD: H , , placed for donor 2FXB 14 CYS N . HBUILD: H , , placed for donor 2FXB 15 GLY N . HBUILD: H , , placed for donor 2FXB 16 ALA N . HBUILD: H , , placed for donor 2FXB 17 CYS N . HBUILD: H , , placed for donor 2FXB 18 GLY N . HBUILD: H , , placed for donor 2FXB 19 ALA N . HBUILD: H , , placed for donor 2FXB 20 ALA N . HBUILD: H , , placed for donor 2FXB 21 ALA N . HBUILD: H , , placed for donor 2FXB 23 ASP N . HBUILD: H , , placed for donor 2FXB 24 ILE N . HBUILD: H , , placed for donor 2FXB 25 TYR N . HBUILD: H , , placed for donor 2FXB 26 ASP N . HBUILD: H , , placed for donor 2FXB 27 TYR N . HBUILD: H , , placed for donor 2FXB 28 ASP N . HBUILD: H , , placed for donor 2FXB 29 GLU N . HBUILD: H , , placed for donor 2FXB 30 ASP N . HBUILD: H , , placed for donor 2FXB 31 GLY N . HBUILD: H , , placed for donor 2FXB 32 ILE N . HBUILD: H , , placed for donor 2FXB 33 ALA N . HBUILD: H , , placed for donor 2FXB 34 TYR N . HBUILD: H , , placed for donor 2FXB 35 VAL N . HBUILD: H , , placed for donor 2FXB 36 THR N . HBUILD: H , , placed for donor 2FXB 37 LEU N . HBUILD: H , , placed for donor 2FXB 38 ASP N . HBUILD: H , , placed for donor 2FXB 39 ASP N . HBUILD: H , , placed for donor 2FXB 40 ASN N . HBUILD: H , , placed for donor 2FXB 41 GLN N . HBUILD: H , , placed for donor 2FXB 42 GLY N . HBUILD: H , , placed for donor 2FXB 43 ILE N . HBUILD: H , , placed for donor 2FXB 44 VAL N . HBUILD: H , , placed for donor 2FXB 45 GLU N . HBUILD: H , , placed for donor 2FXB 46 VAL N . HBUILD: H , , placed for donor 2FXB 48 ASP N . HBUILD: H , , placed for donor 2FXB 49 ILE N . HBUILD: H , , placed for donor 2FXB 50 LEU N . HBUILD: H , , placed for donor 2FXB 51 ILE N . HBUILD: H , , placed for donor 2FXB 52 ASP N . HBUILD: H , , placed for donor 2FXB 53 ASP N . HBUILD: H , , placed for donor 2FXB 54 MET N . HBUILD: H , , placed for donor 2FXB 55 MET N . HBUILD: H , , placed for donor 2FXB 56 ASP N . HBUILD: H , , placed for donor 2FXB 57 ALA N . HBUILD: H , , placed for donor 2FXB 58 PHE N . HBUILD: H , , placed for donor 2FXB 59 GLU N . HBUILD: H , , placed for donor 2FXB 60 GLY N . HBUILD: H , , placed for donor 2FXB 61 CYS N . HBUILD: H , , placed for donor 2FXB 63 THR N . HBUILD: H , , placed for donor 2FXB 64 ASP N . HBUILD: H , , placed for donor 2FXB 65 SER N . HBUILD: H , , placed for donor 2FXB 66 ILE N . HBUILD: H , , placed for donor 2FXB 67 LYS N . HBUILD: H , , placed for donor 2FXB 68 VAL N . HBUILD: H , , placed for donor 2FXB 69 ALA N . HBUILD: H , , placed for donor 2FXB 70 ASP N . HBUILD: H , , placed for donor 2FXB 71 GLU N . HBUILD: H , , placed for donor 2FXB 73 PHE N . HBUILD: H , , placed for donor 2FXB 74 ASP N . HBUILD: H , , placed for donor 2FXB 75 GLY N . HBUILD: H , , placed for donor 2FXB 76 ASP N . HBUILD: H , , placed for donor 2FXB 78 ASN N . HBUILD: H , , placed for donor 2FXB 79 LYS N . HBUILD: H , , placed for donor 2FXB 80 PHE N . HBUILD: H , , placed for donor 2FXB 81 GLU N . HBUILD: HZ1 ,HZ2 ,HZ3 , constructed (spin) for donor 2FXB 2 LYS NZ . HBUILD: HH , , , constructed (spin) for donor 2FXB 3 TYR OH . HBUILD: HG1 , , , constructed (spin) for donor 2FXB 4 THR OG1 . HBUILD: HZ1 ,HZ2 ,HZ3 , constructed (spin) for donor 2FXB 8 LYS NZ . HBUILD: HG1 , , , constructed (spin) for donor 2FXB 10 THR OG1 . HBUILD: HH , , , constructed (spin) for donor 2FXB 25 TYR OH . HBUILD: HH , , , constructed (spin) for donor 2FXB 27 TYR OH . HBUILD: HH , , , constructed (spin) for donor 2FXB 34 TYR OH . HBUILD: HG1 , , , constructed (spin) for donor 2FXB 36 THR OG1 . HBUILD: HD21,HD22, , constructed (spin) for donor 2FXB 40 ASN ND2 . HBUILD: HE21,HE22, , constructed (spin) for donor 2FXB 41 GLN NE2 . HBUILD: HG1 , , , constructed (spin) for donor 2FXB 63 THR OG1 . HBUILD: HG , , , constructed (spin) for donor 2FXB 65 SER OG . HBUILD: HZ1 ,HZ2 ,HZ3 , constructed (spin) for donor 2FXB 67 LYS NZ . HBUILD: HD21,HD22, , constructed (spin) for donor 2FXB 78 ASN ND2 . HBUILD: HZ1 ,HZ2 ,HZ3 , constructed (spin) for donor 2FXB 79 LYS NZ . X-PLOR> X-PLOR> constraints fix=( not hydrogen ) end {* Minimize hydrogen positions. *} SELRPN: 620 atoms have been selected out of 724 X-PLOR> flags include vdw elec end X-PLOR> minimize powell POWELL> nstep=40 POWELL> end POWELL: number of degrees of freedom= 312 NBONDS: generating intra-molecular exclusion list with mode= 5 MAKINB: mode 5 found 1820 exclusions and 1330 interactions(1-4) %atoms "2FXB-4 -THR -HG1 " and "2FXB-25 -TYR -HH " only 1.35 A apart NBONDS: found 25060 intra-atom interactions --------------- cycle= 1 ------ stepsize= 0.0000 ----------------------- | Etotal =2254.733 grad(E)=148.022 E(BOND)=498.137 E(ANGL)=2857.022 | | E(DIHE)=491.189 E(IMPR)=447.427 E(VDW )=168.786 E(ELEC)=-2207.828 | ------------------------------------------------------------------------------- --------------- cycle= 2 ------ stepsize= 0.0001 ----------------------- | Etotal =2236.017 grad(E)=147.887 E(BOND)=499.012 E(ANGL)=2852.175 | | E(DIHE)=491.095 E(IMPR)=447.431 E(VDW )=154.996 E(ELEC)=-2208.692 | ------------------------------------------------------------------------------- --------------- cycle= 3 ------ stepsize= 0.0004 ----------------------- | Etotal =2213.275 grad(E)=147.818 E(BOND)=509.391 E(ANGL)=2843.598 | | E(DIHE)=490.830 E(IMPR)=447.474 E(VDW )=132.965 E(ELEC)=-2210.983 | ------------------------------------------------------------------------------- --------------- cycle= 4 ------ stepsize= 0.0005 ----------------------- | Etotal =2206.060 grad(E)=147.768 E(BOND)=508.395 E(ANGL)=2840.971 | | E(DIHE)=490.602 E(IMPR)=447.586 E(VDW )=132.840 E(ELEC)=-2214.334 | ------------------------------------------------------------------------------- --------------- cycle= 5 ------ stepsize= 0.0008 ----------------------- | Etotal =2201.503 grad(E)=147.749 E(BOND)=508.304 E(ANGL)=2841.200 | | E(DIHE)=490.213 E(IMPR)=447.922 E(VDW )=133.754 E(ELEC)=-2219.891 | ------------------------------------------------------------------------------- --------------- cycle= 6 ------ stepsize= 0.0014 ----------------------- | Etotal =2193.067 grad(E)=147.749 E(BOND)=507.308 E(ANGL)=2842.419 | | E(DIHE)=490.026 E(IMPR)=449.096 E(VDW )=133.737 E(ELEC)=-2229.519 | ------------------------------------------------------------------------------- --------------- cycle= 7 ------ stepsize= 0.0034 ----------------------- | Etotal =2184.458 grad(E)=147.800 E(BOND)=507.740 E(ANGL)=2850.448 | | E(DIHE)=489.813 E(IMPR)=455.148 E(VDW )=134.954 E(ELEC)=-2253.645 | ------------------------------------------------------------------------------- --------------- cycle= 8 ------ stepsize= 0.0035 ----------------------- | Etotal =2200.870 grad(E)=147.999 E(BOND)=531.979 E(ANGL)=2872.001 | | E(DIHE)=489.671 E(IMPR)=473.804 E(VDW )=113.543 E(ELEC)=-2280.128 | ------------------------------------------------------------------------------- --------------- cycle= 9 ------ stepsize= 0.0011 ----------------------- | Etotal =2179.329 grad(E)=147.815 E(BOND)=510.893 E(ANGL)=2855.839 | | E(DIHE)=489.651 E(IMPR)=459.739 E(VDW )=125.171 E(ELEC)=-2261.964 | ------------------------------------------------------------------------------- --------------- cycle= 10 ------ stepsize= 0.0011 ----------------------- | Etotal =2177.720 grad(E)=147.795 E(BOND)=507.833 E(ANGL)=2857.051 | | E(DIHE)=489.460 E(IMPR)=461.687 E(VDW )=126.135 E(ELEC)=-2264.446 | ------------------------------------------------------------------------------- --------------- cycle= 11 ------ stepsize= 0.0009 ----------------------- | Etotal =2177.335 grad(E)=147.785 E(BOND)=505.844 E(ANGL)=2858.118 | | E(DIHE)=489.337 E(IMPR)=463.341 E(VDW )=127.083 E(ELEC)=-2266.389 | ------------------------------------------------------------------------------- --------------- cycle= 12 ------ stepsize= 0.0016 ----------------------- | Etotal =2174.058 grad(E)=147.793 E(BOND)=506.183 E(ANGL)=2857.515 | | E(DIHE)=489.013 E(IMPR)=465.559 E(VDW )=123.703 E(ELEC)=-2267.914 | ------------------------------------------------------------------------------- --------------- cycle= 13 ------ stepsize= 0.0031 ----------------------- | Etotal =2171.515 grad(E)=147.817 E(BOND)=506.487 E(ANGL)=2858.066 | | E(DIHE)=488.989 E(IMPR)=470.453 E(VDW )=118.300 E(ELEC)=-2270.780 | ------------------------------------------------------------------------------- NBONDS: found 25076 intra-atom interactions --------------- cycle= 14 ------ stepsize= 0.0017 ----------------------- | Etotal =2165.964 grad(E)=147.839 E(BOND)=500.751 E(ANGL)=2860.388 | | E(DIHE)=490.679 E(IMPR)=477.624 E(VDW )=114.939 E(ELEC)=-2278.417 | ------------------------------------------------------------------------------- --------------- cycle= 15 ------ stepsize= -0.0002 ----------------------- | Etotal =2165.838 grad(E)=147.832 E(BOND)=500.973 E(ANGL)=2859.928 | | E(DIHE)=490.383 E(IMPR)=476.647 E(VDW )=115.364 E(ELEC)=-2277.457 | ------------------------------------------------------------------------------- --------------- cycle= 16 ------ stepsize= 0.0015 ----------------------- | Etotal =2162.449 grad(E)=147.846 E(BOND)=501.577 E(ANGL)=2858.917 | | E(DIHE)=490.845 E(IMPR)=474.250 E(VDW )=114.772 E(ELEC)=-2277.912 | ------------------------------------------------------------------------------- --------------- cycle= 17 ------ stepsize= 0.0016 ----------------------- | Etotal =2161.233 grad(E)=147.873 E(BOND)=503.845 E(ANGL)=2858.057 | | E(DIHE)=491.457 E(IMPR)=471.984 E(VDW )=114.282 E(ELEC)=-2278.393 | ------------------------------------------------------------------------------- --------------- cycle= 18 ------ stepsize= 0.0026 ----------------------- | Etotal =2156.445 grad(E)=147.858 E(BOND)=502.742 E(ANGL)=2856.683 | | E(DIHE)=494.431 E(IMPR)=467.616 E(VDW )=114.033 E(ELEC)=-2279.059 | ------------------------------------------------------------------------------- --------------- cycle= 19 ------ stepsize= -0.0001 ----------------------- | Etotal =2156.438 grad(E)=147.858 E(BOND)=502.672 E(ANGL)=2856.719 | | E(DIHE)=494.301 E(IMPR)=467.764 E(VDW )=114.014 E(ELEC)=-2279.032 | ------------------------------------------------------------------------------- --------------- cycle= 20 ------ stepsize= 0.0025 ----------------------- | Etotal =2153.752 grad(E)=147.802 E(BOND)=500.937 E(ANGL)=2855.965 | | E(DIHE)=495.321 E(IMPR)=464.262 E(VDW )=112.067 E(ELEC)=-2274.800 | ------------------------------------------------------------------------------- --------------- cycle= 21 ------ stepsize= -0.0005 ----------------------- | Etotal =2153.521 grad(E)=147.810 E(BOND)=500.750 E(ANGL)=2856.053 | | E(DIHE)=495.061 E(IMPR)=464.987 E(VDW )=112.409 E(ELEC)=-2275.739 | ------------------------------------------------------------------------------- --------------- cycle= 22 ------ stepsize= 0.0019 ----------------------- | Etotal =2152.096 grad(E)=147.818 E(BOND)=500.953 E(ANGL)=2855.078 | | E(DIHE)=495.795 E(IMPR)=462.896 E(VDW )=112.536 E(ELEC)=-2275.161 | ------------------------------------------------------------------------------- --------------- cycle= 23 ------ stepsize= 0.0013 ----------------------- | Etotal =2151.833 grad(E)=147.827 E(BOND)=501.329 E(ANGL)=2854.616 | | E(DIHE)=496.341 E(IMPR)=461.676 E(VDW )=112.663 E(ELEC)=-2274.792 | ------------------------------------------------------------------------------- --------------- cycle= 24 ------ stepsize= 0.0032 ----------------------- | Etotal =2151.079 grad(E)=147.838 E(BOND)=501.388 E(ANGL)=2853.650 | | E(DIHE)=496.917 E(IMPR)=460.150 E(VDW )=113.619 E(ELEC)=-2274.644 | ------------------------------------------------------------------------------- --------------- cycle= 25 ------ stepsize= -0.0003 ----------------------- | Etotal =2151.073 grad(E)=147.837 E(BOND)=501.359 E(ANGL)=2853.705 | | E(DIHE)=496.867 E(IMPR)=460.271 E(VDW )=113.527 E(ELEC)=-2274.656 | ------------------------------------------------------------------------------- --------------- cycle= 26 ------ stepsize= 0.0029 ----------------------- | Etotal =2150.309 grad(E)=147.822 E(BOND)=501.628 E(ANGL)=2852.651 | | E(DIHE)=497.911 E(IMPR)=458.995 E(VDW )=113.278 E(ELEC)=-2274.154 | ------------------------------------------------------------------------------- --------------- cycle= 27 ------ stepsize= -0.0001 ----------------------- | Etotal =2150.308 grad(E)=147.822 E(BOND)=501.612 E(ANGL)=2852.671 | | E(DIHE)=497.885 E(IMPR)=459.023 E(VDW )=113.283 E(ELEC)=-2274.166 | ------------------------------------------------------------------------------- --------------- cycle= 28 ------ stepsize= 0.0028 ----------------------- | Etotal =2149.872 grad(E)=147.825 E(BOND)=501.176 E(ANGL)=2852.254 | | E(DIHE)=498.353 E(IMPR)=459.119 E(VDW )=113.396 E(ELEC)=-2274.425 | ------------------------------------------------------------------------------- --------------- cycle= 29 ------ stepsize= -0.0001 ----------------------- | Etotal =2149.871 grad(E)=147.825 E(BOND)=501.180 E(ANGL)=2852.261 | | E(DIHE)=498.341 E(IMPR)=459.116 E(VDW )=113.392 E(ELEC)=-2274.418 | ------------------------------------------------------------------------------- --------------- cycle= 30 ------ stepsize= 0.0028 ----------------------- | Etotal =2149.280 grad(E)=147.830 E(BOND)=501.181 E(ANGL)=2852.028 | | E(DIHE)=498.740 E(IMPR)=459.675 E(VDW )=113.484 E(ELEC)=-2275.829 | ------------------------------------------------------------------------------- NBONDS: found 25074 intra-atom interactions --------------- cycle= 31 ------ stepsize= 0.0011 ----------------------- | Etotal =2149.229 grad(E)=147.833 E(BOND)=501.244 E(ANGL)=2852.052 | | E(DIHE)=498.893 E(IMPR)=459.918 E(VDW )=113.547 E(ELEC)=-2276.424 | ------------------------------------------------------------------------------- --------------- cycle= 32 ------ stepsize= 0.0039 ----------------------- | Etotal =2148.744 grad(E)=147.839 E(BOND)=502.132 E(ANGL)=2852.024 | | E(DIHE)=499.195 E(IMPR)=461.252 E(VDW )=112.859 E(ELEC)=-2278.717 | ------------------------------------------------------------------------------- --------------- cycle= 33 ------ stepsize= -0.0006 ----------------------- | Etotal =2148.727 grad(E)=147.838 E(BOND)=501.950 E(ANGL)=2851.989 | | E(DIHE)=499.158 E(IMPR)=461.033 E(VDW )=112.946 E(ELEC)=-2278.349 | ------------------------------------------------------------------------------- --------------- cycle= 34 ------ stepsize= 0.0024 ----------------------- | Etotal =2148.074 grad(E)=147.831 E(BOND)=501.054 E(ANGL)=2851.919 | | E(DIHE)=499.190 E(IMPR)=461.858 E(VDW )=114.171 E(ELEC)=-2280.118 | ------------------------------------------------------------------------------- --------------- cycle= 35 ------ stepsize= 0.0015 ----------------------- | Etotal =2147.977 grad(E)=147.827 E(BOND)=500.677 E(ANGL)=2851.953 | | E(DIHE)=499.142 E(IMPR)=462.395 E(VDW )=115.033 E(ELEC)=-2281.224 | ------------------------------------------------------------------------------- --------------- cycle= 36 ------ stepsize= 0.0033 ----------------------- | Etotal =2147.362 grad(E)=147.828 E(BOND)=502.090 E(ANGL)=2851.926 | | E(DIHE)=498.758 E(IMPR)=462.901 E(VDW )=114.697 E(ELEC)=-2283.010 | ------------------------------------------------------------------------------- --------------- cycle= 37 ------ stepsize= -0.0005 ----------------------- | Etotal =2147.339 grad(E)=147.827 E(BOND)=501.795 E(ANGL)=2851.903 | | E(DIHE)=498.833 E(IMPR)=462.812 E(VDW )=114.720 E(ELEC)=-2282.723 | ------------------------------------------------------------------------------- NBONDS: found 25079 intra-atom interactions --------------- cycle= 38 ------ stepsize= 0.0027 ----------------------- | Etotal =2147.103 grad(E)=147.828 E(BOND)=501.840 E(ANGL)=2851.852 | | E(DIHE)=498.392 E(IMPR)=462.961 E(VDW )=116.088 E(ELEC)=-2284.029 | ------------------------------------------------------------------------------- --------------- cycle= 39 ------ stepsize= -0.0008 ----------------------- | Etotal =2147.044 grad(E)=147.828 E(BOND)=501.760 E(ANGL)=2851.829 | | E(DIHE)=498.531 E(IMPR)=462.913 E(VDW )=115.656 E(ELEC)=-2283.646 | ------------------------------------------------------------------------------- --------------- cycle= 40 ------ stepsize= 0.0015 ----------------------- | Etotal =2146.648 grad(E)=147.826 E(BOND)=501.082 E(ANGL)=2851.843 | | E(DIHE)=498.288 E(IMPR)=462.645 E(VDW )=116.236 E(ELEC)=-2283.444 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> constraints fix=( not all ) end SELRPN: 0 atoms have been selected out of 724 X-PLOR> X-PLOR> write coordinates output=generatemetal.pdb end ASSFIL: file generatemetal.pdb opened. X-PLOR> X-PLOR> write structure output=generatemetal.psf end ASSFIL: file generatemetal.psf opened. X-PLOR> stop CSTACK: size= 40000 used= 1498 current= 0 HEAP: maximum use= 91569 current use= 0 X-PLOR: total CPU time= 4.9700 s X-PLOR: entry time at 13: 6:31 11-Feb-96 X-PLOR: exit time at 13: 6:36 11-Feb-96