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 10:28:12 X-PLOR>remarks TOPPAR19.INP X-PLOR>remarks test TOPPAR 19 topology and parameter files X-PLOR>remarks Use BPTI2 coordinates with all but 4 water removed. X-PLOR> X-PLOR>rtf @TOPPAR:toph19.pro @TOPPAR:toph19.sol end ASSFIL: file /home/schwitrs/xplor/toppar/toph19.pro opened. RTFRDR>REMARKS TOPH19.PRO ( protein topology ) 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> @TOPPAR:toph19.sol end ASSFIL: file /home/schwitrs/xplor/toppar/toph19.sol opened. RTFRDR>remarks TOPH19.SOL RTFRDR>remarks ========== RTFRDR>remarks topology file for solvent molecules RTFRDR>remarks water models available: TIP3P model RTFRDR> RTFRDR>set echo=false end RTFRDR> end X-PLOR>parameter @TOPPAR:param19.pro @TOPPAR:param19.sol end ASSFIL: file /home/schwitrs/xplor/toppar/param19.pro opened. PARRDR>remark - parameter file PARAM19 - PARRDR>remark PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) PARRDR>remark TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) PARRDR>remark JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 PARRDR> PARRDR>set echo=false end PARRDR> @TOPPAR:param19.sol end ASSFIL: file /home/schwitrs/xplor/toppar/param19.sol opened. PARRDR>remarks PARAM19.SOL (water parameters) PARRDR>remarks =========== PARRDR>remarks available: TIPS3P model PARRDR> PARRDR>set echo=false end PARRDR> end X-PLOR> X-PLOR>segment SEGMENT> name=MAIN SEGMENT> chain CHAIN> @TOPPAR:toph19.pep ASSFIL: file /home/schwitrs/xplor/toppar/toph19.pep opened. CHAIN>REMARKS TOPH19.pep -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>display $cpu 0.17 X-PLOR> X-PLOR>parameter PARRDR> nbonds NBDSET> atom cdie shif vswi cutnb=8.0 ctofnb=7.5 ctonnb=6.5 eps=1.0 NBDSET> e14fac=0.4 wmin=1.5 NBDSET> end %NBDSET-ERR: inconsistent CUTNB, TOLErance, CTOFNB given. Reset. PARRDR>end X-PLOR> X-PLOR>display $cpu 0.17 X-PLOR> X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.170000 sec. ENERGY: after BOND term CPU= 0.170000 sec. ENERGY: after ANGLE term CPU= 0.170000 sec. ENERGY: after DIHEdral term CPU= 0.180000 sec. ENERGY: after IMPRoper term CPU= 0.180000 sec. ENBOND: after parameter lookup CPU= 0.180000 sec. NBONDS: at entry CPU= 0.180000 sec. MAKINB: mode 5 found 2451 exclusions, 999 interactions(1-4) and 1452 GB exclusions NBONDS: after excl. CPU= 0.180000 sec. NBONDS: at exit CPU= 0.180000 sec. ENBOND: after intra interactions CPU= 0.190000 sec. ENBOND: after 1-4 interactions CPU= 0.190000 sec. ENERGY: after NONBonded term CPU= 0.190000 sec. --------------- cycle= 1 -------------------------------------------------- | Etotal =-1676.922 grad(E)=15.679 E(BOND)=93.697 E(ANGL)=70.964 | | E(DIHE)=87.442 E(IMPR)=13.866 E(VDW )=-271.523 E(ELEC)=-1671.370 | ------------------------------------------------------------------------------- X-PLOR>display $elec -1671.37 X-PLOR>display $vdw -271.523 X-PLOR>display $bond 93.6975 X-PLOR>display $angl 70.964 X-PLOR>display $dihe 87.4424 X-PLOR>display $impr 13.8665 X-PLOR> X-PLOR>vector show element ( dx ) ( resid 1 ) SELRPN: 22 atoms have been selected out of 580 ( MAIN ARG 1 HT1 ) 8.3208 ( MAIN ARG 1 HT2 ) 3.4683 ( MAIN ARG 1 N ) 31.526 ( MAIN ARG 1 HT3 ) -0.12353E-01 ( MAIN ARG 1 CA ) -32.994 ( MAIN ARG 1 CB ) -4.1023 ( MAIN ARG 1 CG ) -1.0843 ( MAIN ARG 1 CD ) -18.055 ( MAIN ARG 1 NE ) 33.875 ( MAIN ARG 1 HE ) 1.7869 ( MAIN ARG 1 CZ ) -15.586 ( MAIN ARG 1 NH1 ) -1.8748 ( MAIN ARG 1 HH11 ) 1.6432 ( MAIN ARG 1 HH12 ) 3.5010 ( MAIN ARG 1 NH2 ) -5.7787 ( MAIN ARG 1 HH21 ) 1.4324 ( MAIN ARG 1 HH22 ) 2.8539 ( MAIN ARG 1 C ) -1.7290 ( MAIN ARG 1 O ) -21.572 ( SOLV TIP3 1 OH2 ) 10.319 ( SOLV TIP3 1 H1 ) -15.742 ( SOLV TIP3 1 H2 ) -4.6591 X-PLOR> X-PLOR>stop HEAP: maximum use= 1014988 current use= 939607 X-PLOR: total CPU time= 0.1900 s X-PLOR: entry time at 10:28:12 04-Jun-04 X-PLOR: exit time at 10:28:12 04-Jun-04