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 10:27:44 X-PLOR>remarks ++++++++++++++++PATCHTEST+++++++++++++++++++++++++++++ X-PLOR>remarks Test case for the PATCH command X-PLOR>remarks by Axel Brunger, JAN-1983 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>rtf RTFRDR> RTFRDR> PRESidue HISE ! Patch to change doubly protonated HIS to singly RESIDUE> ! protonated histidine (HE2) RESIDUE> ! has to be patched as REFErence=NIL= RESIDUE> RESIDUE> GROUP RESIDUE> MODIFY ATOM CB TYPE CH2E CHARGE 0.0 END RESIDUE> MODIFY ATOM CG TYPE C CHARGE 0.0 END RESIDUE> GROUP RESIDUE> MODIFY ATOM ND1 TYPE NR CHARGE -0.24 END RESIDUE> MODIFY ATOM CE1 TYPE CR1E CHARGE 0.24 END RESIDUE> GROUP RESIDUE> MODIFY ATOM CD2 TYPE CR1E CHARGE 0.10 END RESIDUE> MODIFY ATOM NE2 TYPE NH1 CHARGE -0.32 END RESIDUE> MODIFY ATOM HE2 TYPE H CHARGE 0.22 END RESIDUE> DELETE ATOM HD1 END RESIDUE> RESIDUE> ADD ACCEPTOR ND1 " " RESIDUE> RESIDUE>END {HISE} RTFRDR> RTFRDR>!-------------------------------------------------------------------------- RTFRDR> RTFRDR>PRES HISD ! Patch to change doubly protonated HIS to singly RESIDUE> ! protonated histidine (HD1) RESIDUE> ! has to be patched as REFErence=NIL= RESIDUE> GROUP RESIDUE> MODIFY ATOM CB TYPE CH2E CHARGE 0.00 END RESIDUE> MODIFY ATOM CG TYPE C CHARGE 0.03 END RESIDUE> GROUP RESIDUE> MODIFY ATOM ND1 TYPE NH1 CHARGE -0.31 END RESIDUE> MODIFY ATOM HD1 TYPE H CHARGE 0.22 END RESIDUE> GROUP RESIDUE> MODIFY ATOM CD2 TYPE CR1E CHARGE 0.09 END RESIDUE> MODIFY ATOM NE2 TYPE NR CHARGE -0.25 END RESIDUE> MODIFY ATOM CE1 TYPE CR1E CHARGE 0.22 END RESIDUE> DELETE ATOM HE2 END RESIDUE> RESIDUE> ADD ACCEPTOR NE2 " " RESIDUE> RESIDUE>END {HISD} RTFRDR> RTFRDR>!----------------------------------------------------------------------- RTFRDR> RTFRDR>PRES HIST ! INVERSE PATCH TO HISD RESIDUE> ! has to be patched as REFErence=NIL= RESIDUE> RESIDUE> GROUP RESIDUE> MODIFY ATOM CB TYPE CH2E CHARGE 0.10 END RESIDUE> MODIFY ATOM CG TYPE C CHARGE 0.15 END RESIDUE> MODIFY ATOM CD2 TYPE CR1E CHARGE 0.20 END RESIDUE> GROUP RESIDUE> MODIFY ATOM ND1 TYPE NH1 CHARGE -0.25 END RESIDUE> MODIFY ATOM HD1 TYPE H CHARGE 0.32 END RESIDUE> GROUP RESIDUE> MODIFY ATOM CE1 TYPE CR1E CHARGE 0.41 END RESIDUE> GROUP RESIDUE> MODIFY ATOM NE2 TYPE NH1 CHARGE -0.25 END RESIDUE> ADD ATOM HE2 TYPE H CHARGE 0.32 END RESIDUE> RESIDUE> ADD BOND NE2 HE2 RESIDUE> RESIDUE> ADD ANGLE HE2 NE2 CD2 RESIDUE> ADD ANGLE HE2 NE2 CE1 RESIDUE> RESIDUE> ADD IMPROPER NE2 CE1 CD2 HE2 RESIDUE> RESIDUE> ADD DONOR HE2 NE2 RESIDUE> DELETE ACCEPTOR NE2 " " RESIDUE> RESIDUE> ADD IC CE1 CD2 *NE2 HE2 0.0 0.0 180.0 0.0 0.0 RESIDUE> RESIDUE>END {HISD} RTFRDR> RTFRDR>!--------------------------------------------------------------------- RTFRDR> RTFRDR> RTFRDR>! the following patch is somewhat strange: RTFRDR>! it shows what happens if one attempts to form groups between RTFRDR>! different residues in different segments RTFRDR> RTFRDR> RTFRDR> PRESidue TES2 RESIDUE> GROUP RESIDUE> ADD ATOM 1XX TYPE C CHARGE 0.00 END RESIDUE> ADD ATOM 1YY TYPE C CHARGE 0.00 END RESIDUE> ADD ATOM 2YY TYPE C CHARGE 0.00 END RESIDUE> MODIFY ATOM 2CA TYPE CH1E CHARGE 0.00 END RESIDUE> RESIDUE> DELETE BOND 1HT1 1N RESIDUE> END {TES2} RTFRDR> RTFRDR>END !RTF X-PLOR> 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>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>cons fix=( atom * * H* ) end SELRPN: 25 atoms have been selected out of 97 X-PLOR> X-PLOR>patch hise refer=NIL=( atom comp 1 * ) setup=true end SELRPN: 15 atoms have been selected out of 97 MAPIC: Atom numbers being modified XPLOR: current counts (number in parenthesis is maximum) NATOM= 96(MAXA= 200) NBOND= 101(MAXB= 200) NTHETA= 151(MAXT= 200) NGRP= 41(MAXGRP= 100) NPHI= 37(MAXP= 100) NIMPHI= 74(MAXIMP= 100) NDON= 24(MAXPAD= 100) NACC= 10(MAXPAD= 100) NNB= 0(MAXNB= 0) X-PLOR>patch hisd refer=NIL=( atom comp 2 * ) setup=true end SELRPN: 13 atoms have been selected out of 96 MAPIC: Atom numbers being modified XPLOR: current counts (number in parenthesis is maximum) NATOM= 95(MAXA= 200) NBOND= 100(MAXB= 200) NTHETA= 149(MAXT= 200) NGRP= 40(MAXGRP= 100) NPHI= 37(MAXP= 100) NIMPHI= 73(MAXIMP= 100) NDON= 23(MAXPAD= 100) NACC= 11(MAXPAD= 100) NNB= 0(MAXNB= 0) X-PLOR>patch hist refer=NIL=( atom comp 2 * ) setup=true end SELRPN: 12 atoms have been selected out of 95 MAPIC: Atom numbers being modified XPLOR: current counts (number in parenthesis is maximum) NATOM= 96(MAXA= 200) NBOND= 101(MAXB= 200) NTHETA= 151(MAXT= 200) NGRP= 41(MAXGRP= 100) NPHI= 37(MAXP= 100) NIMPHI= 74(MAXIMP= 100) NDON= 24(MAXPAD= 100) NACC= 10(MAXPAD= 100) NNB= 0(MAXNB= 0) X-PLOR> X-PLOR>delete DELETE> selection=( atom comp 3 * OR atom comp 4 * OR atom comp 5 * ) SELRPN: 40 atoms have been selected out of 96 DELETE>end MAPIC: Atom numbers being modified XPLOR: current counts (number in parenthesis is maximum) NATOM= 56(MAXA= 200) NBOND= 58(MAXB= 200) NTHETA= 86(MAXT= 200) NGRP= 23(MAXGRP= 100) NPHI= 21(MAXP= 100) NIMPHI= 40(MAXIMP= 100) NDON= 15(MAXPAD= 100) NACC= 6(MAXPAD= 100) NNB= 0(MAXNB= 0) X-PLOR> X-PLOR>patch tes2 refer=1=( atom main 1 * ) refer=2=( atom comp 2 * ) end SELRPN: 15 atoms have been selected out of 56 SELRPN: 13 atoms have been selected out of 56 MAPIC: Atom numbers being modified XPLOR: current counts (number in parenthesis is maximum) NATOM= 59(MAXA= 200) NBOND= 57(MAXB= 200) NTHETA= 86(MAXT= 200) NGRP= 24(MAXGRP= 100) NPHI= 21(MAXP= 100) NIMPHI= 40(MAXIMP= 100) NDON= 15(MAXPAD= 100) NACC= 6(MAXPAD= 100) NNB= 0(MAXNB= 0) X-PLOR> X-PLOR>write psf end PSF 3 !NTITLE REMARKS FILENAME="OUTPUT" REMARKS TOPH11-MACRO for protein sequence REMARKS DATE:04-Jun-04 10:27:44 created by user: [unknown] 59 !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 XX C 0.00000 12.0110 0 7 MAIN 1 HIS YY C 0.00000 12.0110 0 8 COMP 2 HIS YY C 0.00000 12.0110 0 9 COMP 2 HIS CA CH1E 0.00000 13.0190 0 10 MAIN 1 HIS CB CH2E 0.100000 14.0270 0 11 MAIN 1 HIS CG C 0.150000 12.0110 0 12 MAIN 1 HIS CD2 CR1E 0.200000 13.0190 0 13 MAIN 1 HIS ND1 NH1 -0.250000 14.0067 0 14 MAIN 1 HIS HD1 H 0.320000 1.00800 0 15 MAIN 1 HIS CE1 CR1E 0.410000 13.0190 0 16 MAIN 1 HIS NE2 NH1 -0.250000 14.0067 0 17 MAIN 1 HIS HE2 H 0.320000 1.00800 0 18 MAIN 1 HIS C C 0.450000 12.0110 0 19 MAIN 1 HIS O O -0.450000 15.9994 0 20 MAIN 2 HIS N NH1 -0.350000 14.0067 0 21 MAIN 2 HIS H H 0.250000 1.00800 0 22 MAIN 2 HIS CA CH1E 0.100000 13.0190 0 23 MAIN 2 HIS CB CH2E 0.100000 14.0270 0 24 MAIN 2 HIS CG C 0.150000 12.0110 0 25 MAIN 2 HIS CD2 CR1E 0.200000 13.0190 0 26 MAIN 2 HIS ND1 NH1 -0.250000 14.0067 0 27 MAIN 2 HIS HD1 H 0.320000 1.00800 0 28 MAIN 2 HIS CE1 CR1E 0.410000 13.0190 0 29 MAIN 2 HIS NE2 NH1 -0.250000 14.0067 0 30 MAIN 2 HIS HE2 H 0.320000 1.00800 0 31 MAIN 2 HIS C C 0.140000 12.0110 0 32 MAIN 2 HIS OT1 OC -0.570000 15.9994 0 33 MAIN 2 HIS OT2 OC -0.570000 15.9994 0 34 COMP 1 HIS HT1 HC 0.260000 1.00800 0 35 COMP 1 HIS HT2 HC 0.260000 1.00800 0 36 COMP 1 HIS N NH3 0.00000 14.0067 0 37 COMP 1 HIS HT3 HC 0.260000 1.00800 0 38 COMP 1 HIS CA CH1E 0.220000 13.0190 0 39 COMP 1 HIS CB CH2E 0.00000 14.0270 0 40 COMP 1 HIS CG C 0.00000 12.0110 0 41 COMP 1 HIS CD2 CR1E 0.100000 13.0190 0 42 COMP 1 HIS NE2 NH1 -0.320000 14.0067 0 43 COMP 1 HIS HE2 H 0.220000 1.00800 0 44 COMP 1 HIS ND1 NR -0.240000 14.0067 0 45 COMP 1 HIS CE1 CR1E 0.240000 13.0190 0 46 COMP 1 HIS C C 0.450000 12.0110 0 47 COMP 1 HIS O O -0.450000 15.9994 0 48 COMP 2 HIS N NH1 -0.350000 14.0067 0 49 COMP 2 HIS H H 0.250000 1.00800 0 50 COMP 2 HIS CB CH2E 0.100000 14.0270 0 51 COMP 2 HIS CG C 0.150000 12.0110 0 52 COMP 2 HIS CD2 CR1E 0.200000 13.0190 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 ND1 NH1 -0.250000 14.0067 0 57 COMP 2 HIS HD1 H 0.320000 1.00800 0 58 COMP 2 HIS C C 0.450000 12.0110 0 59 COMP 2 HIS O O -0.450000 15.9994 0 57 !NBOND: bonds 3 5 5 18 18 19 5 10 10 11 11 13 11 12 13 14 13 15 12 16 15 16 16 17 2 3 4 3 20 22 22 31 20 21 22 23 23 24 24 26 24 25 26 27 26 28 25 29 28 29 29 30 18 20 31 32 31 33 36 38 38 46 46 47 38 39 39 40 40 44 40 41 44 45 41 42 45 42 42 43 34 36 35 36 37 36 48 9 9 58 58 59 48 49 9 50 50 51 51 56 51 52 56 57 56 53 52 54 53 54 46 48 54 55 86 !NTHETA: angles 3 5 18 3 5 10 5 18 19 18 5 10 5 10 11 10 11 13 10 11 12 13 11 12 11 13 14 11 13 15 11 12 16 14 13 15 13 15 16 12 16 15 12 16 17 15 16 17 1 3 2 2 3 4 2 3 5 1 3 4 1 3 5 4 3 5 20 22 31 22 20 21 20 22 23 31 22 23 22 23 24 23 24 26 23 24 25 26 24 25 24 26 27 24 26 28 24 25 29 27 26 28 26 28 29 25 29 28 25 29 30 28 29 30 5 18 20 19 18 20 18 20 22 18 20 21 22 31 32 22 31 33 32 31 33 36 38 46 36 38 39 38 46 47 46 38 39 38 39 40 39 40 44 39 40 41 44 40 41 40 44 45 40 41 42 44 45 42 41 42 45 41 42 43 45 42 43 34 36 35 35 36 37 35 36 38 34 36 37 34 36 38 37 36 38 48 9 58 9 48 49 48 9 50 9 58 59 58 9 50 9 50 51 50 51 56 50 51 52 56 51 52 51 56 57 51 56 53 51 52 54 57 56 53 56 53 54 52 54 53 38 46 48 47 46 48 46 48 9 46 48 49 55 54 52 55 54 53 21 !NPHI: dihedrals 3 5 10 11 5 10 11 13 2 3 5 18 1 3 5 18 4 3 5 18 20 22 23 24 22 23 24 26 18 20 22 31 3 5 18 20 5 18 20 22 20 22 31 33 36 38 39 40 38 39 40 44 35 36 38 46 34 36 38 46 37 36 38 46 48 9 50 51 9 50 51 56 46 48 9 58 36 38 46 48 38 46 48 9 40 !NIMPHI: impropers 5 3 18 10 11 13 12 10 13 11 15 14 16 12 15 17 11 13 15 16 13 15 16 12 15 16 12 11 16 12 11 13 12 11 13 15 22 20 31 23 24 26 25 23 26 24 28 27 29 25 28 30 24 26 28 29 26 28 29 25 28 29 25 24 29 25 24 26 25 24 26 28 18 5 20 19 20 18 22 21 31 22 33 32 38 36 46 39 40 44 41 39 42 41 45 43 40 44 45 42 44 45 42 41 45 42 41 40 42 41 40 44 41 40 44 45 9 48 58 50 51 56 52 50 56 51 53 57 51 56 53 54 56 53 54 52 53 54 52 51 54 52 51 56 52 51 56 53 46 38 48 47 48 46 9 49 54 53 52 55 15 !NDON: donors 13 14 16 17 3 1 3 2 3 4 20 21 26 27 29 30 42 43 36 34 36 35 36 37 48 49 56 57 54 55 6 !NACC: acceptors 19 18 32 31 33 31 47 46 59 58 44 0 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 24 0 !NGRP 0 0 0 5 0 0 9 0 0 12 0 0 14 0 0 15 0 0 17 0 0 19 0 0 22 0 0 25 0 0 27 0 0 28 0 0 30 0 0 33 0 0 38 0 0 40 0 0 43 0 0 45 0 0 47 0 0 49 0 0 52 0 0 53 0 0 55 0 0 57 0 0 X-PLOR> X-PLOR> X-PLOR>{* now test the handling of explicit exclusion lists during patch *} X-PLOR>{* ============================================================== *} X-PLOR> X-PLOR>delete selection=( all ) end SELRPN: 59 atoms have been selected out of 59 MAPIC: Atom numbers being modified 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) X-PLOR>RTF RTFRDR> RESIDUE EX1 RESIDUE> ATOM ABCD EXCLUSION=( B C ) END RESIDUE> ATOM B EXCLUSION=( D ) END RESIDUE> ATOM C END RESIDUE> ATOM D END RESIDUE> ATOM E END RESIDUE> END %RTFIO-warning: undefined masses in residue EX1 %RTFIO-ERR: there are undefined masses. RTFRDR> RTFRDR> RESIDUE EX2 RESIDUE> ATOM A EXCLUSION=( B ) END RESIDUE> ATOM B END RESIDUE> END %RTFIO-warning: undefined masses in residue EX2 %RTFIO-ERR: there are undefined masses. RTFRDR> RTFRDR> PRESIDUE EXP RESIDUE> MODIFY ATOM 1ABCD EXCLUSION=( 1B 1C 1E 1X ) END RESIDUE> MODIFY ATOM 2A EXCLUSION=( 1B 1ABCD 1X ) END RESIDUE> ADD ATOM 1X EXCLUSION=( 2B ) END RESIDUE> ADD BOND 1ABCD 2A RESIDUE> END RTFRDR>END X-PLOR> X-PLOR>SEGMENT SEGMENT> NAME=TEST SEGMENT> CHAIN CHAIN> SEQUENCE SEQUENCE> EX1 EX2 SEQUence-element (terminate with END) = END CHAIN> END SEGMENT>END SEGMNT: 2 residues were inserted into segment "TEST" XPLOR: current counts (number in parenthesis is maximum) NATOM= 7(MAXA= 200) NBOND= 0(MAXB= 200) NTHETA= 0(MAXT= 200) NGRP= 2(MAXGRP= 100) NPHI= 0(MAXP= 100) NIMPHI= 0(MAXIMP= 100) NDON= 0(MAXPAD= 100) NACC= 0(MAXPAD= 100) NNB= 4(MAXNB= 100) X-PLOR> X-PLOR>WRITE PSF END PSF 3 !NTITLE REMARKS FILENAME="OUTPUT" REMARKS TOPH11-MACRO for protein sequence REMARKS DATE:04-Jun-04 10:27:44 created by user: [unknown] 7 !NATOM 1 TEST 1 EX1 ABCD 0.00000 9999.00 0 2 TEST 1 EX1 B 0.00000 9999.00 0 3 TEST 1 EX1 C 0.00000 9999.00 0 4 TEST 1 EX1 D 0.00000 9999.00 0 5 TEST 1 EX1 E 0.00000 9999.00 0 6 TEST 2 EX2 A 0.00000 9999.00 0 7 TEST 2 EX2 B 0.00000 9999.00 0 0 !NBOND: bonds 0 !NTHETA: angles 0 !NPHI: dihedrals 0 !NIMPHI: impropers 0 !NDON: donors 0 !NACC: acceptors 4 !NNB 2 3 4 7 2 3 3 3 3 4 4 2 0 !NGRP 0 0 0 5 0 0 X-PLOR> X-PLOR>PATCH EXP REFERENCE=1=( RESID 1 ) REFERENCE=2=( RESID 2 ) END SELRPN: 5 atoms have been selected out of 7 SELRPN: 2 atoms have been selected out of 7 MAPIC: Atom numbers being modified XPLOR: current counts (number in parenthesis is maximum) NATOM= 8(MAXA= 200) NBOND= 1(MAXB= 200) NTHETA= 0(MAXT= 200) NGRP= 2(MAXGRP= 100) NPHI= 0(MAXP= 100) NIMPHI= 0(MAXIMP= 100) NDON= 0(MAXPAD= 100) NACC= 0(MAXPAD= 100) NNB= 9(MAXNB= 100) X-PLOR> X-PLOR>WRITE PSF END PSF 3 !NTITLE REMARKS FILENAME="OUTPUT" REMARKS TOPH11-MACRO for protein sequence REMARKS DATE:04-Jun-04 10:27:44 created by user: [unknown] 8 !NATOM 1 TEST 1 EX1 ABCD 0.00000 9999.00 0 2 TEST 1 EX1 X 0.00000 9999.00 0 3 TEST 1 EX1 B 0.00000 9999.00 0 4 TEST 1 EX1 C 0.00000 9999.00 0 5 TEST 1 EX1 D 0.00000 9999.00 0 6 TEST 1 EX1 E 0.00000 9999.00 0 7 TEST 2 EX2 A 0.00000 9999.00 0 8 TEST 2 EX2 B 0.00000 9999.00 0 1 !NBOND: bonds 1 7 0 !NTHETA: angles 0 !NPHI: dihedrals 0 !NIMPHI: impropers 0 !NDON: donors 0 !NACC: acceptors 9 !NNB 3 4 6 2 8 5 3 1 2 4 5 6 6 6 6 9 9 2 0 !NGRP 0 0 0 6 0 0 X-PLOR> X-PLOR> X-PLOR>struc reset 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= 100) X-PLOR> X-PLOR> X-PLOR>remarks Test multiple links. X-PLOR> X-PLOR>set echo=false end %RTFIO-warning: undefined masses in residue ALA %RTFIO-ERR: there are undefined masses. %RTFIO-warning: undefined masses in residue GLY %RTFIO-ERR: there are undefined masses. X-PLOR> X-PLOR>segment SEGMENT> name=" " SEGMENT> chain CHAIN> link L1 head - ALA tail + * end CHAIN> link L2 head - * tail + ALA end CHAIN> link L3 head - * tail + * end CHAIN>! sequence FOR GLY GLY ALA end CHAIN> coordinates SEGMNT: sequence read from coordinate file COOR>ATOM 1 C ALA 1 9999.0009999.0009999.000 1.00 0.00 CHAIN> end SEGMENT>end SEGMNT: 4 residues were inserted into segment " " XPLOR: current counts (number in parenthesis is maximum) NATOM= 22(MAXA= 200) NBOND= 18(MAXB= 200) NTHETA= 0(MAXT= 200) NGRP= 4(MAXGRP= 100) NPHI= 3(MAXP= 100) NIMPHI= 2(MAXIMP= 100) NDON= 0(MAXPAD= 100) NACC= 0(MAXPAD= 100) NNB= 0(MAXNB= 100) X-PLOR> X-PLOR>write structure end PSF 3 !NTITLE REMARKS FILENAME="OUTPUT" REMARKS Test multiple links. REMARKS DATE:04-Jun-04 10:27:44 created by user: [unknown] 22 !NATOM 1 1 ALA N NH1 -0.350000 9999.00 0 2 1 ALA H H 0.250000 9999.00 0 3 1 ALA CA CH1A 0.100000 9999.00 0 4 1 ALA CB CH3E 0.00000 9999.00 0 5 1 ALA C C 0.550000 9999.00 0 6 1 ALA O O -0.550000 9999.00 0 7 2 GLY N NH1 -0.350000 9999.00 0 8 2 GLY H H 0.250000 9999.00 0 9 2 GLY CA CH1A 0.100000 9999.00 0 10 2 GLY C C 0.550000 9999.00 0 11 2 GLY O O -0.550000 9999.00 0 12 3 GLY N NH1 -0.350000 9999.00 0 13 3 GLY H H 0.250000 9999.00 0 14 3 GLY CA CH1A 0.100000 9999.00 0 15 3 GLY C C 0.550000 9999.00 0 16 3 GLY O O -0.550000 9999.00 0 17 4 ALA N NH1 -0.350000 9999.00 0 18 4 ALA H H 0.250000 9999.00 0 19 4 ALA CA CH1A 0.100000 9999.00 0 20 4 ALA CB CH3E 0.00000 9999.00 0 21 4 ALA C C 0.550000 9999.00 0 22 4 ALA O O -0.550000 9999.00 0 18 !NBOND: bonds 1 3 3 5 5 6 1 2 3 4 7 9 9 10 10 11 7 8 12 14 14 15 15 16 12 13 17 19 19 21 21 22 17 18 19 20 0 !NTHETA: angles 3 !NPHI: dihedrals 6 5 7 8 7 9 10 12 15 17 19 21 2 !NIMPHI: impropers 7 5 9 8 10 9 12 11 0 !NDON: donors 0 !NACC: acceptors 0 !NNB 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 !NGRP 0 0 0 6 0 0 11 0 0 16 0 0 X-PLOR> X-PLOR>stop HEAP: maximum use= 892978 current use= 870447 X-PLOR: total CPU time= 0.1600 s X-PLOR: entry time at 10:27:44 04-Jun-04 X-PLOR: exit time at 10:27:44 04-Jun-04