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 10:27:46 X-PLOR>remarks ++++++++++++++++PSFTEST+++++++++++++++++++++++++++++ X-PLOR>remarks by Axel Brunger, MAY-1984 X-PLOR> X-PLOR>rtf @TOPPAR:toph11.pro 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> end X-PLOR>parameter @TOPPAR:param11.pro 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> end X-PLOR> X-PLOR>SEGMENT SEGMENT> NAME=MAIN SEGMENT> SETUP=TRUE 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> SEQUENCE SEQUENCE> HIS HIS MAPIC: Atom numbers being modified SEQUence-element (terminate with END) = END MAPIC: Atom numbers being modified CHAIN> END SEGMENT>END SEGMNT: 2 residues were inserted into segment "MAIN" XPLOR: current counts (number in parenthesis is maximum) NATOM= 29(MAXA= 200) NBOND= 30(MAXB= 100) NTHETA= 45(MAXT= 100) NGRP= 12(MAXGRP= 100) NPHI= 11(MAXP= 100) NIMPHI= 21(MAXIMP= 100) NDON= 8(MAXPAD= 100) NACC= 3(MAXPAD= 100) NNB= 0(MAXNB= 0) X-PLOR> X-PLOR>SEGMENT SEGMENT> NAME=COMP SEGMENT> SETUP=TRUE 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> SEQUENCE SEQUENCE> HIS HIS HIS HIS HIS MAPIC: Atom numbers being modified SEQUence-element (terminate with END) = END MAPIC: Atom numbers being modified CHAIN> END SEGMENT>END SEGMNT: 5 residues were inserted into segment "COMP" XPLOR: current counts (number in parenthesis is maximum) NATOM= 97(MAXA= 200) NBOND= 102(MAXB= 200) NTHETA= 153(MAXT= 200) NGRP= 42(MAXGRP= 100) NPHI= 37(MAXP= 100) NIMPHI= 75(MAXIMP= 100) NDON= 25(MAXPAD= 100) NACC= 9(MAXPAD= 100) NNB= 0(MAXNB= 0) X-PLOR> X-PLOR>write psf output=testpsf.dat end ASSFIL: file testpsf.dat opened. X-PLOR>close testpsf.dat end %X-PLOR>-ERR: File testpsf.dat was not open. X-PLOR> X-PLOR>structure reset @testpsf.dat end XPLOR: current counts (number in parenthesis is maximum) NATOM= 0(MAXA= 200) NBOND= 0(MAXB= 200) NTHETA= 0(MAXT= 200) NGRP= 0(MAXGRP= 100) NPHI= 0(MAXP= 100) NIMPHI= 0(MAXIMP= 100) NDON= 0(MAXPAD= 100) NACC= 0(MAXPAD= 100) NNB= 0(MAXNB= 0) ASSFIL: file testpsf.dat opened. STRUcture>PSF REMARKS FILENAME="testpsf.dat" REMARKS TOPH11-MACRO for protein sequence REMARKS DATE:04-Jun-04 10:27:46 created by user: [unknown] XPLOR: current counts (number in parenthesis is maximum) NATOM= 97(MAXA= 200) NBOND= 102(MAXB= 200) NTHETA= 153(MAXT= 200) NGRP= 42(MAXGRP= 100) NPHI= 37(MAXP= 100) NIMPHI= 75(MAXIMP= 100) NDON= 25(MAXPAD= 100) NACC= 9(MAXPAD= 100) NNB= 0(MAXNB= 100) STRUcture> end X-PLOR> X-PLOR>write psf end PSF 3 !NTITLE REMARKS FILENAME="OUTPUT" REMARKS TOPH11-MACRO for protein sequence REMARKS DATE:04-Jun-04 10:27:46 created by user: [unknown] 97 !NATOM 1 MAIN 1 HIS HT1 HC 0.260000 1.00800 0 2 MAIN 1 HIS HT2 HC 0.260000 1.00800 0 3 MAIN 1 HIS N NH3 0.00000 14.0067 0 4 MAIN 1 HIS HT3 HC 0.260000 1.00800 0 5 MAIN 1 HIS CA CH1E 0.220000 13.0190 0 6 MAIN 1 HIS CB CH2E 0.100000 14.0270 0 7 MAIN 1 HIS CG C 0.150000 12.0110 0 8 MAIN 1 HIS CD2 CR1E 0.200000 13.0190 0 9 MAIN 1 HIS ND1 NH1 -0.250000 14.0067 0 10 MAIN 1 HIS HD1 H 0.320000 1.00800 0 11 MAIN 1 HIS CE1 CR1E 0.410000 13.0190 0 12 MAIN 1 HIS NE2 NH1 -0.250000 14.0067 0 13 MAIN 1 HIS HE2 H 0.320000 1.00800 0 14 MAIN 1 HIS C C 0.450000 12.0110 0 15 MAIN 1 HIS O O -0.450000 15.9994 0 16 MAIN 2 HIS N NH1 -0.350000 14.0067 0 17 MAIN 2 HIS H H 0.250000 1.00800 0 18 MAIN 2 HIS CA CH1E 0.100000 13.0190 0 19 MAIN 2 HIS CB CH2E 0.100000 14.0270 0 20 MAIN 2 HIS CG C 0.150000 12.0110 0 21 MAIN 2 HIS CD2 CR1E 0.200000 13.0190 0 22 MAIN 2 HIS ND1 NH1 -0.250000 14.0067 0 23 MAIN 2 HIS HD1 H 0.320000 1.00800 0 24 MAIN 2 HIS CE1 CR1E 0.410000 13.0190 0 25 MAIN 2 HIS NE2 NH1 -0.250000 14.0067 0 26 MAIN 2 HIS HE2 H 0.320000 1.00800 0 27 MAIN 2 HIS C C 0.140000 12.0110 0 28 MAIN 2 HIS OT1 OC -0.570000 15.9994 0 29 MAIN 2 HIS OT2 OC -0.570000 15.9994 0 30 COMP 1 HIS HT1 HC 0.260000 1.00800 0 31 COMP 1 HIS HT2 HC 0.260000 1.00800 0 32 COMP 1 HIS N NH3 0.00000 14.0067 0 33 COMP 1 HIS HT3 HC 0.260000 1.00800 0 34 COMP 1 HIS CA CH1E 0.220000 13.0190 0 35 COMP 1 HIS CB CH2E 0.100000 14.0270 0 36 COMP 1 HIS CG C 0.150000 12.0110 0 37 COMP 1 HIS CD2 CR1E 0.200000 13.0190 0 38 COMP 1 HIS ND1 NH1 -0.250000 14.0067 0 39 COMP 1 HIS HD1 H 0.320000 1.00800 0 40 COMP 1 HIS CE1 CR1E 0.410000 13.0190 0 41 COMP 1 HIS NE2 NH1 -0.250000 14.0067 0 42 COMP 1 HIS HE2 H 0.320000 1.00800 0 43 COMP 1 HIS C C 0.450000 12.0110 0 44 COMP 1 HIS O O -0.450000 15.9994 0 45 COMP 2 HIS N NH1 -0.350000 14.0067 0 46 COMP 2 HIS H H 0.250000 1.00800 0 47 COMP 2 HIS CA CH1E 0.100000 13.0190 0 48 COMP 2 HIS CB CH2E 0.100000 14.0270 0 49 COMP 2 HIS CG C 0.150000 12.0110 0 50 COMP 2 HIS CD2 CR1E 0.200000 13.0190 0 51 COMP 2 HIS ND1 NH1 -0.250000 14.0067 0 52 COMP 2 HIS HD1 H 0.320000 1.00800 0 53 COMP 2 HIS CE1 CR1E 0.410000 13.0190 0 54 COMP 2 HIS NE2 NH1 -0.250000 14.0067 0 55 COMP 2 HIS HE2 H 0.320000 1.00800 0 56 COMP 2 HIS C C 0.450000 12.0110 0 57 COMP 2 HIS O O -0.450000 15.9994 0 58 COMP 3 HIS N NH1 -0.350000 14.0067 0 59 COMP 3 HIS H H 0.250000 1.00800 0 60 COMP 3 HIS CA CH1E 0.100000 13.0190 0 61 COMP 3 HIS CB CH2E 0.100000 14.0270 0 62 COMP 3 HIS CG C 0.150000 12.0110 0 63 COMP 3 HIS CD2 CR1E 0.200000 13.0190 0 64 COMP 3 HIS ND1 NH1 -0.250000 14.0067 0 65 COMP 3 HIS HD1 H 0.320000 1.00800 0 66 COMP 3 HIS CE1 CR1E 0.410000 13.0190 0 67 COMP 3 HIS NE2 NH1 -0.250000 14.0067 0 68 COMP 3 HIS HE2 H 0.320000 1.00800 0 69 COMP 3 HIS C C 0.450000 12.0110 0 70 COMP 3 HIS O O -0.450000 15.9994 0 71 COMP 4 HIS N NH1 -0.350000 14.0067 0 72 COMP 4 HIS H H 0.250000 1.00800 0 73 COMP 4 HIS CA CH1E 0.100000 13.0190 0 74 COMP 4 HIS CB CH2E 0.100000 14.0270 0 75 COMP 4 HIS CG C 0.150000 12.0110 0 76 COMP 4 HIS CD2 CR1E 0.200000 13.0190 0 77 COMP 4 HIS ND1 NH1 -0.250000 14.0067 0 78 COMP 4 HIS HD1 H 0.320000 1.00800 0 79 COMP 4 HIS CE1 CR1E 0.410000 13.0190 0 80 COMP 4 HIS NE2 NH1 -0.250000 14.0067 0 81 COMP 4 HIS HE2 H 0.320000 1.00800 0 82 COMP 4 HIS C C 0.450000 12.0110 0 83 COMP 4 HIS O O -0.450000 15.9994 0 84 COMP 5 HIS N NH1 -0.350000 14.0067 0 85 COMP 5 HIS H H 0.250000 1.00800 0 86 COMP 5 HIS CA CH1E 0.100000 13.0190 0 87 COMP 5 HIS CB CH2E 0.100000 14.0270 0 88 COMP 5 HIS CG C 0.150000 12.0110 0 89 COMP 5 HIS CD2 CR1E 0.200000 13.0190 0 90 COMP 5 HIS ND1 NH1 -0.250000 14.0067 0 91 COMP 5 HIS HD1 H 0.320000 1.00800 0 92 COMP 5 HIS CE1 CR1E 0.410000 13.0190 0 93 COMP 5 HIS NE2 NH1 -0.250000 14.0067 0 94 COMP 5 HIS HE2 H 0.320000 1.00800 0 95 COMP 5 HIS C C 0.140000 12.0110 0 96 COMP 5 HIS OT1 OC -0.570000 15.9994 0 97 COMP 5 HIS OT2 OC -0.570000 15.9994 0 102 !NBOND: bonds 3 5 5 14 14 15 5 6 6 7 7 9 7 8 9 10 9 11 8 12 11 12 12 13 1 3 2 3 4 3 16 18 18 27 16 17 18 19 19 20 20 22 20 21 22 23 22 24 21 25 24 25 25 26 14 16 27 28 27 29 32 34 34 43 43 44 34 35 35 36 36 38 36 37 38 39 38 40 37 41 40 41 41 42 30 32 31 32 33 32 45 47 47 56 56 57 45 46 47 48 48 49 49 51 49 50 51 52 51 53 50 54 53 54 54 55 43 45 58 60 60 69 69 70 58 59 60 61 61 62 62 64 62 63 64 65 64 66 63 67 66 67 67 68 56 58 71 73 73 82 82 83 71 72 73 74 74 75 75 77 75 76 77 78 77 79 76 80 79 80 80 81 69 71 84 86 86 95 84 85 86 87 87 88 88 90 88 89 90 91 90 92 89 93 92 93 93 94 82 84 95 96 95 97 153 !NTHETA: angles 3 5 14 3 5 6 5 14 15 14 5 6 5 6 7 6 7 9 6 7 8 9 7 8 7 9 10 7 9 11 7 8 12 10 9 11 9 11 12 8 12 11 8 12 13 11 12 13 1 3 2 2 3 4 2 3 5 1 3 4 1 3 5 4 3 5 16 18 27 18 16 17 16 18 19 27 18 19 18 19 20 19 20 22 19 20 21 22 20 21 20 22 23 20 22 24 20 21 25 23 22 24 22 24 25 21 25 24 21 25 26 24 25 26 5 14 16 15 14 16 14 16 18 14 16 17 18 27 28 18 27 29 28 27 29 32 34 43 32 34 35 34 43 44 43 34 35 34 35 36 35 36 38 35 36 37 38 36 37 36 38 39 36 38 40 36 37 41 39 38 40 38 40 41 37 41 40 37 41 42 40 41 42 30 32 31 31 32 33 31 32 34 30 32 33 30 32 34 33 32 34 45 47 56 47 45 46 45 47 48 47 56 57 56 47 48 47 48 49 48 49 51 48 49 50 51 49 50 49 51 52 49 51 53 49 50 54 52 51 53 51 53 54 50 54 53 50 54 55 53 54 55 34 43 45 44 43 45 43 45 47 43 45 46 58 60 69 60 58 59 58 60 61 60 69 70 69 60 61 60 61 62 61 62 64 61 62 63 64 62 63 62 64 65 62 64 66 62 63 67 65 64 66 64 66 67 63 67 66 63 67 68 66 67 68 47 56 58 57 56 58 56 58 60 56 58 59 71 73 82 73 71 72 71 73 74 73 82 83 82 73 74 73 74 75 74 75 77 74 75 76 77 75 76 75 77 78 75 77 79 75 76 80 78 77 79 77 79 80 76 80 79 76 80 81 79 80 81 60 69 71 70 69 71 69 71 73 69 71 72 84 86 95 86 84 85 84 86 87 95 86 87 86 87 88 87 88 90 87 88 89 90 88 89 88 90 91 88 90 92 88 89 93 91 90 92 90 92 93 89 93 92 89 93 94 92 93 94 73 82 84 83 82 84 82 84 86 82 84 85 86 95 96 86 95 97 96 95 97 37 !NPHI: dihedrals 3 5 6 7 5 6 7 9 2 3 5 14 1 3 5 14 4 3 5 14 16 18 19 20 18 19 20 22 14 16 18 27 3 5 14 16 5 14 16 18 16 18 27 29 32 34 35 36 34 35 36 38 31 32 34 43 30 32 34 43 33 32 34 43 45 47 48 49 47 48 49 51 43 45 47 56 32 34 43 45 34 43 45 47 58 60 61 62 60 61 62 64 56 58 60 69 45 47 56 58 47 56 58 60 71 73 74 75 73 74 75 77 69 71 73 82 58 60 69 71 60 69 71 73 84 86 87 88 86 87 88 90 82 84 86 95 71 73 82 84 73 82 84 86 84 86 95 97 75 !NIMPHI: impropers 5 3 14 6 7 9 8 6 9 7 11 10 12 8 11 13 7 9 11 12 9 11 12 8 11 12 8 7 12 8 7 9 8 7 9 11 18 16 27 19 20 22 21 19 22 20 24 23 25 21 24 26 20 22 24 25 22 24 25 21 24 25 21 20 25 21 20 22 21 20 22 24 14 5 16 15 16 14 18 17 27 18 29 28 34 32 43 35 36 38 37 35 38 36 40 39 41 37 40 42 36 38 40 41 38 40 41 37 40 41 37 36 41 37 36 38 37 36 38 40 47 45 56 48 49 51 50 48 51 49 53 52 54 50 53 55 49 51 53 54 51 53 54 50 53 54 50 49 54 50 49 51 50 49 51 53 43 34 45 44 45 43 47 46 60 58 69 61 62 64 63 61 64 62 66 65 67 63 66 68 62 64 66 67 64 66 67 63 66 67 63 62 67 63 62 64 63 62 64 66 56 47 58 57 58 56 60 59 73 71 82 74 75 77 76 74 77 75 79 78 80 76 79 81 75 77 79 80 77 79 80 76 79 80 76 75 80 76 75 77 76 75 77 79 69 60 71 70 71 69 73 72 86 84 95 87 88 90 89 87 90 88 92 91 93 89 92 94 88 90 92 93 90 92 93 89 92 93 89 88 93 89 88 90 89 88 90 92 82 73 84 83 84 82 86 85 95 86 97 96 25 !NDON: donors 9 10 12 13 3 1 3 2 3 4 16 17 22 23 25 26 38 39 41 42 32 30 32 31 32 33 45 46 51 52 54 55 58 59 64 65 67 68 71 72 77 78 80 81 84 85 90 91 93 94 9 !NACC: acceptors 15 14 28 27 29 27 44 43 57 56 70 69 83 82 96 95 97 95 0 !NNB 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 0 !NGRP 0 0 0 5 0 0 8 0 0 10 0 0 11 0 0 13 0 0 15 0 0 18 0 0 21 0 0 23 0 0 24 0 0 26 0 0 29 0 0 34 0 0 37 0 0 39 0 0 40 0 0 42 0 0 44 0 0 47 0 0 50 0 0 52 0 0 53 0 0 55 0 0 57 0 0 60 0 0 63 0 0 65 0 0 66 0 0 68 0 0 70 0 0 73 0 0 76 0 0 78 0 0 79 0 0 81 0 0 83 0 0 86 0 0 89 0 0 91 0 0 92 0 0 94 0 0 X-PLOR> X-PLOR>close testpsf.dat end %X-PLOR>-ERR: File testpsf.dat was not open. X-PLOR>open testpsf.dat access=append end close testpsf.dat disp=delete end ASSFIL: file testpsf.dat opened. X-PLOR> X-PLOR>stop HEAP: maximum use= 892978 current use= 870447 X-PLOR: total CPU time= 0.1400 s X-PLOR: entry time at 10:27:46 04-Jun-04 X-PLOR: exit time at 10:27:46 04-Jun-04