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 EGROUPES X-PLOR>remarks test vectorized group energy routines X-PLOR>remarks using BPTI coordinates with all but 4 water removed. X-PLOR>remarks by Axel Brunger, 22-MAR-84 X-PLOR> X-PLOR>rtf @TOPPAR:toph11.pro @TOPPAR:toph11.wat end ASSFIL: file /home/schwitrs/xplor/toppar/toph11.pro opened. RTFRDR>REMARKS TOPH11.PRO ( from TOPH10.INP) 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 DNA/RNA atoms appended . RTFRDR>REMARKS few atoms never referenced switched off. RTFRDR>REMARKS Default for HIStidines is the doubly protonated state RTFRDR> RTFRDR>set echo=false end RTFRDR> @TOPPAR:toph11.wat end ASSFIL: file /home/schwitrs/xplor/toppar/toph11.wat opened. RTFRDR>remarks TOPH11.WAT RTFRDR>remarks ========== RTFRDR>remarks topology file for water RTFRDR>remarks available: TIP3P model RTFRDR> RTFRDR>set echo=false end RTFRDR> end X-PLOR>parameter @TOPPAR:param11.pro @TOPPAR:param11.wat end ASSFIL: file /home/schwitrs/xplor/toppar/param11.pro opened. PARRDR>REMARKS PARAM11.PRO ( from PARAM6A ) PARRDR>REMARKS =========== PARRDR>REMARKS PROTEIN PARAMETERS: PARRDR>REMARKS PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) PARRDR>REMARKS TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) PARRDR>REMARKS LENNARD-JONES NONBONDED PARAMETERS WITH SPECIAL TREATMENT OF 1:4 PARRDR>REMARKS CARBON-CARBON INTERACTIONS: JORGENSON ET. AL. PARRDR>REMARKS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 PARRDR>REMARKS PARRDR>set echo=false end PARRDR> @TOPPAR:param11.wat end ASSFIL: file /home/schwitrs/xplor/toppar/param11.wat opened. PARRDR>remarks PARAM11.WAT (water parameters) PARRDR>remarks =========== PARRDR>remarks available: TIPS3P model PARRDR>set echo=false end PARRDR> end X-PLOR> X-PLOR>SEGMENT SEGMENT> NAME=MAIN SEGMENT> CHAIN CHAIN> @TOPPAR:toph11.pep ASSFIL: file /home/schwitrs/xplor/toppar/toph11.pep opened. CHAIN>REMARKS TOPH11-MACRO for protein sequence CHAIN>SET ECHO=FALSE END CHAIN> { PTI sequence } CHAIN> SEQUENCE SEQUENCE> ARG PRO ASP PHE CYS LEU GLU PRO PRO TYR THR GLY PRO CYS LYS ALA MAPIC: Atom numbers being modified SEQUence-element (terminate with END) = ARG ILE ILE ARG TYR PHE TYR ASN ALA LYS ALA GLY LEU CYS GLN THR SEQUence-element (terminate with END) = PHE VAL TYR GLY GLY CYS ARG ALA LYS ARG ASN ASN PHE LYS SER ALA SEQUence-element (terminate with END) = GLU ASP CYS MET ARG THR CYS GLY GLY ALA SEQUence-element (terminate with END) = END MAPIC: Atom numbers being modified CHAIN> END SEGMENT>END SEGMNT: 58 residues were inserted into segment "MAIN" XPLOR: current counts (number in parenthesis is maximum) NATOM= 568(MAXA= 800) NBOND= 579(MAXB= 800) NTHETA= 828(MAXT= 1600) NGRP= 222(MAXGRP= 400) NPHI= 342(MAXP= 400) NIMPHI= 259(MAXIMP= 400) NDON= 114(MAXPAD= 200) NACC= 79(MAXPAD= 200) NNB= 24(MAXNB= 100) X-PLOR> X-PLOR>PATCH DISU REFERENCE 1 ( ATOM MAIN 5 * ) REFERENCE 2 ( ATOM MAIN 55 * ) END SELRPN: 7 atoms have been selected out of 568 SELRPN: 7 atoms have been selected out of 568 MAPIC: Atom numbers being modified XPLOR: current counts (number in parenthesis is maximum) NATOM= 568(MAXA= 800) NBOND= 580(MAXB= 800) NTHETA= 830(MAXT= 1600) NGRP= 222(MAXGRP= 400) NPHI= 345(MAXP= 400) NIMPHI= 259(MAXIMP= 400) NDON= 114(MAXPAD= 200) NACC= 79(MAXPAD= 200) NNB= 24(MAXNB= 100) X-PLOR>PATCH DISU REFERENCE 1 ( ATOM MAIN 14 * ) REFERENCE 2 ( ATOM MAIN 38 * ) END SELRPN: 7 atoms have been selected out of 568 SELRPN: 7 atoms have been selected out of 568 MAPIC: Atom numbers being modified XPLOR: current counts (number in parenthesis is maximum) NATOM= 568(MAXA= 800) NBOND= 581(MAXB= 800) NTHETA= 832(MAXT= 1600) NGRP= 222(MAXGRP= 400) NPHI= 348(MAXP= 400) NIMPHI= 259(MAXIMP= 400) NDON= 114(MAXPAD= 200) NACC= 79(MAXPAD= 200) NNB= 24(MAXNB= 100) X-PLOR>PATCH DISU REFERENCE 1 ( ATOM MAIN 30 * ) REFERENCE 2 ( ATOM MAIN 51 * ) END SELRPN: 7 atoms have been selected out of 568 SELRPN: 7 atoms have been selected out of 568 MAPIC: Atom numbers being modified XPLOR: current counts (number in parenthesis is maximum) NATOM= 568(MAXA= 800) NBOND= 582(MAXB= 800) NTHETA= 834(MAXT= 1600) NGRP= 222(MAXGRP= 400) NPHI= 351(MAXP= 400) NIMPHI= 259(MAXIMP= 400) NDON= 114(MAXPAD= 200) NACC= 79(MAXPAD= 200) NNB= 24(MAXNB= 100) X-PLOR> X-PLOR>SEGMENT SEGMENT> NAME=SOLV SEGMENT> MOLECULE NAME=TIP3 NUMBER=4 END SEGMENT>END SEGMNT: 4 residues were inserted into segment "SOLV" XPLOR: current counts (number in parenthesis is maximum) NATOM= 580(MAXA= 800) NBOND= 590(MAXB= 800) NTHETA= 838(MAXT= 1600) NGRP= 226(MAXGRP= 400) NPHI= 351(MAXP= 400) NIMPHI= 259(MAXIMP= 400) NDON= 114(MAXPAD= 200) NACC= 79(MAXPAD= 200) NNB= 24(MAXNB= 100) X-PLOR> X-PLOR>coor COOR> remarks PTI TEST CASE COORDINATES (SAME AS COORDINATES USED IN ORIGINAL COOR> remarks NORMAL MODE CALCULATION). COOR> remarks OBTAINED USING HARMONIC CONSTRAINTS. COOR> COOR> natoms 580 COOR> 1 1 ARG HT1 13.62071 -4.74562 3.69478 MAIN 1 0.00000 X-PLOR> X-PLOR>COOR COPY END COOR: selected main coordinates copied to comp X-PLOR> X-PLOR>set SET> timer=2 SET>end X-PLOR> X-PLOR>parameter PARRDR> HBONDS HBDSET> DCUT=4.5 DOFF=4.0 DON=3.5 HBDSET> ACUT=90.0 AOFF=70.0 AON=50.0 HBDSET> END %HBDSET-ERR: inconsistent DCUT, TOLErance, DOFF given. Reset. PARRDR> NBONDS NBDSET> GROUP CDIE TRUNCATION CUTNB=8.0 NBDSET> END PARRDR>end X-PLOR> X-PLOR>DISPLAY $CPU 0.16 X-PLOR> X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.160000 sec. ENERGY: after BOND term CPU= 0.160000 sec. ENERGY: after ANGLE term CPU= 0.160000 sec. ENERGY: after DIHEdral term CPU= 0.160000 sec. ENERGY: after IMPRoper term CPU= 0.160000 sec. ENBOND: after parameter lookup CPU= 0.160000 sec. NBONDS: at entry CPU= 0.160000 sec. MAKINB: mode 5 found 2451 exclusions, 999 interactions(1-4) and 1452 GB exclusions NBONDS: after excl. CPU= 0.170000 sec. NBONDS: at exit CPU= 0.170000 sec. ENBOND: after intra interactions CPU= 0.170000 sec. ENBOND: after 1-4 interactions CPU= 0.170000 sec. ENERGY: after NONBonded term CPU= 0.170000 sec. HBONDS: allocating space for 570 h-bond interactions. HBONDS: 8619 distance exclusions and 242 angle exclusions HBONDS: 0 fixed h-bonds, currently 137 h-bonds present EHBOND: after h-bond search CPU= 0.170000 sec. ENERGY: after HBONd term CPU= 0.170000 sec. --------------- cycle= 1 -------------------------------------------------- | Etotal =-667.782 grad(E)=15.203 E(BOND)=93.697 E(ANGL)=70.964 | | E(DIHE)=87.442 E(IMPR)=13.866 E(VDW )=-294.920 E(ELEC)=-566.069 | | E(HBON)=-72.764 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>VECTOR SHOW ELEMENT ( DX ) ( RESID 3 ) SELRPN: 12 atoms have been selected out of 580 ( MAIN ASP 3 N ) 26.880 ( MAIN ASP 3 H ) -3.8809 ( MAIN ASP 3 CA ) -17.003 ( MAIN ASP 3 CB ) -8.0716 ( MAIN ASP 3 CG ) 16.837 ( MAIN ASP 3 OD1 ) -3.5517 ( MAIN ASP 3 OD2 ) -3.1706 ( MAIN ASP 3 C ) -24.618 ( MAIN ASP 3 O ) 5.0950 ( SOLV TIP3 3 OH2 ) -13.159 ( SOLV TIP3 3 H1 ) 10.325 ( SOLV TIP3 3 H2 ) -0.26521E-01 X-PLOR>VECTOR SHOW ELEMENT ( DY ) ( RESID 3 ) SELRPN: 12 atoms have been selected out of 580 ( MAIN ASP 3 N ) 35.845 ( MAIN ASP 3 H ) 1.9826 ( MAIN ASP 3 CA ) -19.491 ( MAIN ASP 3 CB ) 3.3344 ( MAIN ASP 3 CG ) -6.6119 ( MAIN ASP 3 OD1 ) 5.7152 ( MAIN ASP 3 OD2 ) -4.9867 ( MAIN ASP 3 C ) 36.427 ( MAIN ASP 3 O ) -12.380 ( SOLV TIP3 3 OH2 ) -10.677 ( SOLV TIP3 3 H1 ) -0.85002E-01 ( SOLV TIP3 3 H2 ) 14.784 X-PLOR>VECTOR SHOW ELEMENT ( DZ ) ( RESID 3 ) SELRPN: 12 atoms have been selected out of 580 ( MAIN ASP 3 N ) 27.073 ( MAIN ASP 3 H ) -1.8051 ( MAIN ASP 3 CA ) -17.324 ( MAIN ASP 3 CB ) -3.2027 ( MAIN ASP 3 CG ) 4.7223 ( MAIN ASP 3 OD1 ) 6.7468 ( MAIN ASP 3 OD2 ) -10.344 ( MAIN ASP 3 C ) -4.1367 ( MAIN ASP 3 O ) 18.445 ( SOLV TIP3 3 OH2 ) -1.7296 ( SOLV TIP3 3 H1 ) 7.8656 ( SOLV TIP3 3 H2 ) 2.3826 X-PLOR> X-PLOR> X-PLOR>STOP HEAP: maximum use= 1010921 current use= 939607 X-PLOR: total CPU time= 0.1800 s X-PLOR: entry time at 10:27:21 04-Jun-04 X-PLOR: exit time at 10:27:21 04-Jun-04