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 ENERTEST.INP X-PLOR>remarks test energy evaluation under various conditions X-PLOR>remarks Using BPTI2 coordinates with all but 4 water removed. 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>DISPLAY $CPU 0.19 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>end X-PLOR> X-PLOR>DISPLAY $CPU 0.19 X-PLOR> X-PLOR>parameter PARRDR> NBONDS NBDSET> ATOM CDIE SHIF VSWI CUTNB=8.0 CTOFNB=7.5 CTONNB=6.5 NBDSET> END %NBDSET-ERR: inconsistent CUTNB, TOLErance, CTOFNB given. Reset. PARRDR>END X-PLOR> X-PLOR>DISPLAY $CPU 0.19 X-PLOR> X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.190000 sec. ENERGY: after BOND term CPU= 0.190000 sec. ENERGY: after ANGLE term CPU= 0.190000 sec. ENERGY: after DIHEdral term CPU= 0.190000 sec. ENERGY: after IMPRoper term CPU= 0.190000 sec. ENBOND: after parameter lookup CPU= 0.190000 sec. NBONDS: at entry CPU= 0.190000 sec. MAKINB: mode 5 found 2451 exclusions, 999 interactions(1-4) and 1452 GB exclusions NBONDS: after excl. CPU= 0.190000 sec. NBONDS: at exit CPU= 0.200000 sec. ENBOND: after intra interactions CPU= 0.200000 sec. ENBOND: after 1-4 interactions CPU= 0.200000 sec. ENERGY: after NONBonded term CPU= 0.200000 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= 0.200000 sec. ENERGY: after HBONd term CPU= 0.200000 sec. --------------- cycle= 1 -------------------------------------------------- | Etotal =-582.190 grad(E)=15.237 E(BOND)=93.697 E(ANGL)=70.964 | | E(DIHE)=87.442 E(IMPR)=13.866 E(VDW )=-269.674 E(ELEC)=-505.723 | | E(HBON)=-72.764 | ------------------------------------------------------------------------------- X-PLOR>display $elec -505.723 X-PLOR>display $vdw -269.674 X-PLOR>display $hbon -72.7636 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> X-PLOR>flags exclude * include dihe end X-PLOR> X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.200000 sec. ENERGY: after DIHEdral term CPU= 0.200000 sec. --------------- cycle= 2 -------------------------------------------------- | Etotal =87.442 grad(E)=1.623 E(DIHE)=87.442 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>flags exclude * include bond angl impr hbon end X-PLOR> X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.200000 sec. ENERGY: after BOND term CPU= 0.200000 sec. ENERGY: after ANGLE term CPU= 0.200000 sec. ENERGY: after IMPRoper term CPU= 0.200000 sec. ENERGY: after HBONd term CPU= 0.200000 sec. --------------- cycle= 3 -------------------------------------------------- | Etotal =105.764 grad(E)=15.545 E(BOND)=93.697 E(ANGL)=70.964 | | E(IMPR)=13.866 E(HBON)=-72.764 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR> X-PLOR>parameter PARRDR> nbonds NBDSET> cutnb=11.5 ctofnb=10.5 ctonnb=9.5 atom rdiel switch NBDSET> eps=2.0 vswitch nbxm=5 NBDSET> end PARRDR>end X-PLOR> X-PLOR>flags exclude * include vdw elec end X-PLOR> X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.200000 sec. ENBOND: after parameter lookup CPU= 0.200000 sec. NBONDS: at entry CPU= 0.200000 sec. MAKINB: mode 5 found 2451 exclusions, 999 interactions(1-4) and 1452 GB exclusions NBONDS: after excl. CPU= 0.210000 sec. NBONDS: at exit CPU= 0.210000 sec. ENBOND: after intra interactions CPU= 0.220000 sec. ENBOND: after 1-4 interactions CPU= 0.220000 sec. ENERGY: after NONBonded term CPU= 0.220000 sec. --------------- cycle= 4 -------------------------------------------------- | Etotal =-489.005 grad(E)=4.184 E(VDW )=-323.528 E(ELEC)=-165.477 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>{* now check fixing of atoms *} X-PLOR>{* ========================= *} X-PLOR> X-PLOR>set timer=0 end X-PLOR>flags include vdw elec dihe impr hbon bond angle end X-PLOR> X-PLOR>cons interaction=( resid 1 )=( all ) end SELRPN: 22 atoms have been selected out of 580 SELRPN: 580 atoms have been selected out of 580 X-PLOR> X-PLOR>energy end MAKINB: mode 5 found 86 exclusions, 35 interactions(1-4) and 51 GB exclusions HBONDS: allocating space for 181 h-bond interactions. HBONDS: 714 distance exclusions and 13 angle exclusions HBONDS: 8260 fixed h-bonds, currently 11 h-bonds present --------------- cycle= 5 -------------------------------------------------- | Etotal =-37.128 grad(E)=2.612 E(BOND)=2.492 E(ANGL)=3.244 | | E(DIHE)=5.132 E(IMPR)=1.390 E(VDW )=-13.867 E(ELEC)=-31.863 | | E(HBON)=-3.655 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>cons interaction=( resid 1 )=( previous ) end SELRPN: 22 atoms have been selected out of 580 SELRPN: 22 atoms have been selected out of 580 X-PLOR>energy end MAKINB: mode 5 found 72 exclusions, 26 interactions(1-4) and 46 GB exclusions HBONDS: allocating space for 17 h-bond interactions. HBONDS: 5 distance exclusions and 2 angle exclusions HBONDS: 8990 fixed h-bonds, currently 1 h-bonds present --------------- cycle= 6 -------------------------------------------------- | Etotal =6.983 grad(E)=2.228 E(BOND)=2.379 E(ANGL)=1.557 | | E(DIHE)=4.428 E(IMPR)=0.378 E(VDW )=-0.357 E(ELEC)=-1.401 | | E(HBON)=0.000 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>stop HEAP: maximum use= 1051497 current use= 939607 X-PLOR: total CPU time= 0.2300 s X-PLOR: entry time at 10:27:21 04-Jun-04 X-PLOR: exit time at 10:27:21 04-Jun-04