remarks ++++++++++++++++PATCHTEST+++++++++++++++++++++++++++++ remarks Test case for the PATCH command remarks by Axel Brunger, JAN-1983 topology @CNS_TOPPAR:protein.top end parameter @CNS_TOPPAR:protein.param end topology PRESidue HISE ! Patch to change doubly protonated HIS to singly ! protonated histidine (HE2) ! has to be patched as REFErence=NIL= GROUP MODIFY ATOM CB TYPE CH2E CHARGE 0.0 END MODIFY ATOM CG TYPE C CHARGE 0.0 END GROUP MODIFY ATOM ND1 TYPE NR CHARGE -0.24 END MODIFY ATOM CE1 TYPE CR1E CHARGE 0.24 END GROUP MODIFY ATOM CD2 TYPE CR1E CHARGE 0.10 END MODIFY ATOM NE2 TYPE NH1 CHARGE -0.32 END MODIFY ATOM HE2 TYPE H CHARGE 0.22 END DELETE ATOM HD1 END ADD ACCEPTOR ND1 " " END {HISE} !-------------------------------------------------------------------------- PRES HISD ! Patch to change doubly protonated HIS to singly ! protonated histidine (HD1) ! has to be patched as REFErence=NIL= GROUP MODIFY ATOM CB TYPE CH2E CHARGE 0.00 END MODIFY ATOM CG TYPE C CHARGE 0.03 END GROUP MODIFY ATOM ND1 TYPE NH1 CHARGE -0.31 END MODIFY ATOM HD1 TYPE H CHARGE 0.22 END GROUP MODIFY ATOM CD2 TYPE CR1E CHARGE 0.09 END MODIFY ATOM NE2 TYPE NR CHARGE -0.25 END MODIFY ATOM CE1 TYPE CR1E CHARGE 0.22 END DELETE ATOM HE2 END ADD ACCEPTOR NE2 " " END {HISD} !----------------------------------------------------------------------- PRES HIST ! INVERSE PATCH TO HISD ! has to be patched as REFErence=NIL= GROUP MODIFY ATOM CB TYPE CH2E CHARGE 0.10 END MODIFY ATOM CG TYPE C CHARGE 0.15 END MODIFY ATOM CD2 TYPE CR1E CHARGE 0.20 END GROUP MODIFY ATOM ND1 TYPE NH1 CHARGE -0.25 END MODIFY ATOM HD1 TYPE H CHARGE 0.32 END GROUP MODIFY ATOM CE1 TYPE CR1E CHARGE 0.41 END GROUP MODIFY ATOM NE2 TYPE NH1 CHARGE -0.25 END ADD ATOM HE2 TYPE H CHARGE 0.32 END ADD BOND NE2 HE2 ADD ANGLE HE2 NE2 CD2 ADD ANGLE HE2 NE2 CE1 ADD IMPROPER NE2 CE1 CD2 HE2 ADD DONOR HE2 NE2 DELETE ACCEPTOR NE2 " " END {HISD} !--------------------------------------------------------------------- ! the following patch is somewhat strange: ! it shows what happens if one attempts to form groups between ! different residues in different segments PRESidue TES2 GROUP ADD ATOM 1XX TYPE C CHARGE 0.00 END ADD ATOM 1YY TYPE C CHARGE 0.00 END ADD ATOM 2YY TYPE C CHARGE 0.00 END MODIFY ATOM 2CA TYPE CH1E CHARGE 0.00 END DELETE BOND 1HT1 1N END {TES2} END !topology SEGMENT NAME=MAIN CHAIN @CNS_TOPPAR:protein.link SEQUENCE HIS HIS END END END SEGMENT NAME=COMP CHAIN @CNS_TOPPAR:protein.link SEQUENCE HIS HIS HIS HIS HIS END END END fix selection=( atom * * H* ) end patch hise refer=NIL=( atom comp 1 * ) end patch hisd refer=NIL=( atom comp 2 * ) end patch hist refer=NIL=( atom comp 2 * ) end delete selection=( atom comp 3 * OR atom comp 4 * OR atom comp 5 * ) end patch tes2 refer=1=( atom main 1 * ) refer=2=( atom comp 2 * ) end write structure end {* now test the handling of explicit exclusion lists during patch *} {* ============================================================== *} delete selection=( all ) end topology RESIDUE EX1 ATOM ABCD EXCLUSION=( B C ) END ATOM B EXCLUSION=( D ) END ATOM C END ATOM D END ATOM E END END RESIDUE EX2 ATOM A EXCLUSION=( B ) END ATOM B END END PRESIDUE EXP MODIFY ATOM 1ABCD EXCLUSION=( 1B 1C 1E 1X ) END MODIFY ATOM 2A EXCLUSION=( 1B 1ABCD 1X ) END ADD ATOM 1X EXCLUSION=( 2B ) END ADD BOND 1ABCD 2A END END SEGMENT NAME=TEST CHAIN SEQUENCE EX1 EX2 END END END WRITE STRUCTURE END PATCH EXP REFERENCE=1=( RESID 1 ) REFERENCE=2=( RESID 2 ) END WRITE STRUCTURE END struc reset end remarks Test multiple links. set echo=false end topology reset RESIdue ALA ATOM N TYPE=NH1 CHARge=-0.35 END ATOM H TYPE=H CHARge= 0.25 END ATOM CA TYPE=CH1A CHARge= 0.10 END ATOM CB TYPE=CH3E CHARge= 0.00 END ATOM C TYPE=C CHARge= 0.55 END !# ATOM O TYPE=O CHARge=-0.55 END !# BOND N CA BOND CA C BOND C O BOND N H BOND CA CB END {ALA} !------------------------------------------------------------------ RESIdue GLY ATOM N TYPE=NH1 CHARge=-0.35 END ATOM H TYPE=H CHARge= 0.25 END ATOM CA TYPE=CH1A CHARge= 0.10 END ATOM C TYPE=C CHARge= 0.55 END ATOM O TYPE=O CHARge=-0.55 END BOND N CA BOND CA C BOND C O BOND N H END {VAL} !--------------------------------------------------------------------- PRESidue L1 ADD DIHEDRAL -O -C +N +H ADD IMPRoper +N -C +CA +H {planar +N} END !--------------------------------------------------------------------- PRESidue L2 ADD DIHEDRAL -C +N +CA +C END !--------------------------------------------------------------------- PRESidue L3 ADD DIHEDRAL -N -CA -C +N ADD IMPRoper -C -CA +N -O {planar -C} END end set echo=true end segment name=" " chain link L1 head - ALA tail + GLY end link L1 head - ALA tail + ALA end link L2 head - GLY tail + ALA end ! sequence FOR GLY GLY ALA end coordinates ATOM 1 C ALA 1 9999.0009999.0009999.000 1.00 0.00 ATOM 2 O ALA 1 9999.0009999.0009999.000 1.00 0.00 ATOM 3 N GLY 2 9999.0009999.0009999.000 1.00 0.00 ATOM 4 H GLY 2 9999.0009999.0009999.000 1.00 0.00 ATOM 5 CA GLY 2 9999.0009999.0009999.000 1.00 0.00 ATOM 6 C GLY 2 9999.0009999.0009999.000 1.00 0.00 ATOM 7 O GLY 2 9999.0009999.0009999.000 1.00 0.00 ATOM 8 N GLY 3 9999.0009999.0009999.000 1.00 0.00 ATOM 9 H GLY 3 9999.0009999.0009999.000 1.00 0.00 ATOM 10 CA GLY 3 9999.0009999.0009999.000 1.00 0.00 ATOM 11 C GLY 3 9999.0009999.0009999.000 1.00 0.00 ATOM 12 O GLY 3 9999.0009999.0009999.000 1.00 0.00 ATOM 13 N ALA 4 9999.0009999.0009999.000 1.00 0.00 ATOM 14 H ALA 4 9999.0009999.0009999.000 1.00 0.00 ATOM 15 CA ALA 4 9999.0009999.0009999.000 1.00 0.00 ATOM 16 CB ALA 4 9999.0009999.0009999.000 1.00 0.00 ATOM 17 C ALA 4 9999.0009999.0009999.000 1.00 0.00 ATOM 18 O ALA 4 9999.0009999.0009999.000 1.00 0.00 END end end write structure end structure reset end topology reset end topology @CNS_TOPPAR:protein.top @CNS_TOPPAR:carbohydrate.top @CNS_TOPPAR:dna-rna.top end {- test convert and separate features -} segment chain separate=true convert=true @CNS_TOPPAR:protein.link set message=all end coordinates ATOM 1 N HIS A 64 -11.280 54.459 20.936 1.00140.77 N ATOM 2 CA HIS A 64 -10.236 53.634 20.232 1.00137.33 C ATOM 3 C HIS A 64 -10.811 52.425 19.442 1.00134.53 C ATOM 4 O HIS A 64 -10.991 52.498 18.217 1.00135.08 O ATOM 5 CB HIS A 64 -9.148 53.196 21.227 1.00135.24 C ATOM 6 CG HIS A 64 -7.763 53.254 20.665 1.00134.40 C ATOM 7 ND1 HIS A 64 -7.075 54.439 20.507 1.00137.35 N ATOM 8 CD2 HIS A 64 -6.938 52.279 20.215 1.00131.28 C ATOM 9 CE1 HIS A 64 -5.886 54.189 19.985 1.00136.12 C ATOM 10 NE2 HIS A 64 -5.777 52.886 19.799 1.00132.45 N ATOM 11 N MET A 65 -11.074 51.319 20.142 1.00131.84 N ATOM 12 CA MET A 65 -11.731 50.151 19.552 1.00129.54 C ATOM 13 C MET A 65 -13.187 50.163 19.956 1.00131.31 C ATOM 14 O MET A 65 -13.506 50.306 21.136 1.00132.20 O ATOM 15 CB MET A 65 -11.122 48.849 20.064 1.00125.76 C ATOM 16 CG MET A 65 -9.618 48.791 20.118 1.00124.28 C ATOM 17 SD MET A 65 -9.086 47.068 20.145 1.00120.04 S ATOM 18 CE MET A 65 -7.353 47.260 20.553 1.00119.49 C ATOM 19 N GLU A 66 -14.073 50.012 18.980 1.00132.14 N ATOM 20 CA GLU A 66 -15.502 50.053 19.245 1.00134.38 C ATOM 21 C GLU A 66 -16.232 49.124 18.300 1.00133.34 C ATOM 22 O GLU A 66 -17.065 49.550 17.509 1.00136.02 O ATOM 23 CB GLU A 66 -16.051 51.479 19.108 1.00139.02 C ATOM 24 CG GLU A 66 -15.819 52.383 20.305 1.00141.05 C ATOM 25 CD GLU A 66 -14.490 53.100 20.233 1.00140.96 C ATOM 26 OE1 GLU A 66 -14.224 53.759 19.203 1.00142.53 O ATOM 27 OE2 GLU A 66 -13.718 53.004 21.212 1.00139.64 O ATOM 28 N LEU A 67 -15.926 47.842 18.400 1.00129.75 N ATOM 29 CA LEU A 67 -16.499 46.853 17.503 1.00128.58 C ATOM 30 C LEU A 67 -18.018 46.752 17.516 1.00131.09 C ATOM 31 O LEU A 67 -18.737 47.694 17.865 1.00134.60 O ATOM 32 CB LEU A 67 -15.917 45.480 17.815 1.00124.59 C ATOM 33 CG LEU A 67 -14.904 44.959 16.808 1.00122.12 C ATOM 34 CD1 LEU A 67 -14.001 43.994 17.510 1.00118.82 C ATOM 35 CD2 LEU A 67 -15.612 44.298 15.623 1.00122.19 C ATOM 36 N ALA A 68 -18.483 45.579 17.097 1.00129.49 N ATOM 37 CA ALA A 68 -19.861 45.164 17.256 1.00131.40 C ATOM 38 C ALA A 68 -19.879 43.638 17.245 1.00128.34 C ATOM 39 O ALA A 68 -18.847 42.994 17.494 1.00124.96 O ATOM 40 CB ALA A 68 -20.725 45.736 16.139 1.00134.82 C ATOM 41 N LEU A 69 -21.058 43.070 16.989 1.00129.88 N ATOM 42 CA LEU A 69 -21.202 41.641 16.726 1.00127.63 C ATOM 43 C LEU A 69 -22.416 41.377 15.815 1.00130.25 C ATOM 44 O LEU A 69 -23.512 41.068 16.282 1.00132.34 O ATOM 45 CB LEU A 69 -21.245 40.840 18.038 1.00126.23 C ATOM 46 CG LEU A 69 -20.680 39.410 18.116 1.00122.72 C ATOM 47 CD1 LEU A 69 -21.687 38.406 17.597 1.00123.52 C ATOM 48 CD2 LEU A 69 -19.325 39.243 17.414 1.00119.65 C ATOM 49 N ASN A 70 -22.179 41.522 14.511 1.00130.40 N ATOM 50 CA ASN A 70 -23.160 41.321 13.446 1.00133.00 C ATOM 51 C ASN A 70 -22.485 40.507 12.340 1.00130.52 C ATOM 52 O ASN A 70 -21.256 40.459 12.299 1.00127.55 O ATOM 53 CB ASN A 70 -23.577 42.692 12.894 1.00137.00 C ATOM 54 CG ASN A 70 -25.026 42.726 12.427 1.00141.33 C ATOM 55 OD1 ASN A 70 -25.314 42.416 11.265 1.00142.41 O ATOM 56 ND2 ASN A 70 -25.957 43.059 13.350 1.00144.08 N ATOM 1 N HIS B 64 -11.280 54.459 20.936 1.00140.77 N ATOM 2 CA HIS B 64 -10.236 53.634 20.232 1.00137.33 C ATOM 3 C HIS B 64 -10.811 52.425 19.442 1.00134.53 C ATOM 4 O HIS B 64 -10.991 52.498 18.217 1.00135.08 O ATOM 5 CB HIS B 64 -9.148 53.196 21.227 1.00135.24 C ATOM 6 CG HIS B 64 -7.763 53.254 20.665 1.00134.40 C ATOM 7 ND1 HIS B 64 -7.075 54.439 20.507 1.00137.35 N ATOM 8 CD2 HIS B 64 -6.938 52.279 20.215 1.00131.28 C ATOM 9 CE1 HIS B 64 -5.886 54.189 19.985 1.00136.12 C ATOM 10 NE2 HIS B 64 -5.777 52.886 19.799 1.00132.45 N ATOM 11 N MET B 65 -11.074 51.319 20.142 1.00131.84 N ATOM 12 CA MET B 65 -11.731 50.151 19.552 1.00129.54 C ATOM 13 C MET B 65 -13.187 50.163 19.956 1.00131.31 C ATOM 14 O MET B 65 -13.506 50.306 21.136 1.00132.20 O ATOM 15 CB MET B 65 -11.122 48.849 20.064 1.00125.76 C ATOM 16 CG MET B 65 -9.618 48.791 20.118 1.00124.28 C ATOM 17 SD MET B 65 -9.086 47.068 20.145 1.00120.04 S ATOM 18 CE MET B 65 -7.353 47.260 20.553 1.00119.49 C ATOM 19 N GLU B 66 -14.073 50.012 18.980 1.00132.14 N ATOM 20 CA GLU B 66 -15.502 50.053 19.245 1.00134.38 C ATOM 21 C GLU B 66 -16.232 49.124 18.300 1.00133.34 C ATOM 22 O GLU B 66 -17.065 49.550 17.509 1.00136.02 O ATOM 23 CB GLU B 66 -16.051 51.479 19.108 1.00139.02 C ATOM 24 CG GLU B 66 -15.819 52.383 20.305 1.00141.05 C ATOM 25 CD GLU B 66 -14.490 53.100 20.233 1.00140.96 C ATOM 26 OE1 GLU B 66 -14.224 53.759 19.203 1.00142.53 O ATOM 27 OE2 GLU B 66 -13.718 53.004 21.212 1.00139.64 O ATOM 28 N LEU B 67 -15.926 47.842 18.400 1.00129.75 N ATOM 29 CA LEU B 67 -16.499 46.853 17.503 1.00128.58 C ATOM 30 C LEU B 67 -18.018 46.752 17.516 1.00131.09 C ATOM 31 O LEU B 67 -18.737 47.694 17.865 1.00134.60 O ATOM 32 CB LEU B 67 -15.917 45.480 17.815 1.00124.59 C ATOM 33 CG LEU B 67 -14.904 44.959 16.808 1.00122.12 C ATOM 34 CD1 LEU B 67 -14.001 43.994 17.510 1.00118.82 C ATOM 35 CD2 LEU B 67 -15.612 44.298 15.623 1.00122.19 C ATOM 36 N ALA B 68 -18.483 45.579 17.097 1.00129.49 N ATOM 37 CA ALA B 68 -19.861 45.164 17.256 1.00131.40 C ATOM 38 C ALA B 68 -19.879 43.638 17.245 1.00128.34 C ATOM 39 O ALA B 68 -18.847 42.994 17.494 1.00124.96 O ATOM 40 CB ALA B 68 -20.725 45.736 16.139 1.00134.82 C ATOM 41 N LEU B 69 -21.058 43.070 16.989 1.00129.88 N ATOM 42 CA LEU B 69 -21.202 41.641 16.726 1.00127.63 C ATOM 43 C LEU B 69 -22.416 41.377 15.815 1.00130.25 C ATOM 44 O LEU B 69 -23.512 41.068 16.282 1.00132.34 O ATOM 45 CB LEU B 69 -21.245 40.840 18.038 1.00126.23 C ATOM 46 CG LEU B 69 -20.680 39.410 18.116 1.00122.72 C ATOM 47 CD1 LEU B 69 -21.687 38.406 17.597 1.00123.52 C ATOM 48 CD2 LEU B 69 -19.325 39.243 17.414 1.00119.65 C ATOM 49 N ASN B 70 -22.179 41.522 14.511 1.00130.40 N ATOM 50 CA ASN B 70 -23.160 41.321 13.446 1.00133.00 C ATOM 51 C ASN B 70 -22.485 40.507 12.340 1.00130.52 C ATOM 52 O ASN B 70 -21.256 40.459 12.299 1.00127.55 O ATOM 53 CB ASN B 70 -23.577 42.692 12.894 1.00137.00 C ATOM 54 CG ASN B 70 -25.026 42.726 12.427 1.00141.33 C ATOM 55 OD1 ASN B 70 -25.314 42.416 11.265 1.00142.41 O ATOM 56 ND2 ASN B 70 -25.957 43.059 13.350 1.00144.08 N ATOM 2473 C1 NAG B1500 -26.443 44.423 13.287 1.00148.44 C ATOM 2474 C2 NAG B1500 -27.797 44.186 13.960 1.00151.73 C ATOM 2475 C3 NAG B1500 -28.476 45.410 14.573 1.00156.31 C ATOM 2476 C4 NAG B1500 -27.485 46.464 15.110 1.00155.28 C ATOM 2477 C5 NAG B1500 -26.287 46.572 14.150 1.00152.35 C ATOM 2478 C6 NAG B1500 -25.233 47.615 14.540 1.00151.55 C ATOM 2479 C7 NAG B1500 -28.843 42.344 12.908 1.00151.95 C ATOM 2480 C8 NAG B1500 -29.806 41.705 13.869 1.00153.38 C ATOM 2481 N2 NAG B1500 -28.711 43.653 12.984 1.00154.16 N ATOM 2482 O3 NAG B1500 -29.334 44.923 15.598 1.00157.61 O ATOM 2483 O4 NAG B1500 -28.118 47.721 15.303 1.00160.30 O ATOM 2484 O5 NAG B1500 -25.685 45.295 14.095 1.00147.63 O ATOM 2485 O6 NAG B1500 -24.464 47.987 13.405 1.00151.01 O ATOM 2486 O7 NAG B1500 -28.191 41.674 12.112 1.00149.05 O ATOM 2487 C1 NAG B1501 -7.705 55.528 13.365 1.00143.72 C ATOM 2488 C2 NAG B1501 -8.328 56.362 14.502 1.00145.97 C ATOM 2489 C3 NAG B1501 -7.331 57.329 15.156 1.00148.03 C ATOM 2490 C4 NAG B1501 -5.981 56.685 15.423 1.00145.09 C ATOM 2491 C5 NAG B1501 -5.506 55.948 14.165 1.00143.37 C ATOM 2492 C6 NAG B1501 -4.175 55.227 14.362 1.00140.65 C ATOM 2493 C7 NAG B1501 -10.626 57.197 14.598 1.00150.67 C ATOM 2494 C8 NAG B1501 -11.102 58.562 15.050 1.00155.52 C ATOM 2495 N2 NAG B1501 -9.436 57.134 13.967 1.00149.77 N ATOM 2496 O3 NAG B1501 -7.832 57.811 16.381 1.00149.26 O ATOM 2497 O4 NAG B1501 -5.094 57.708 15.834 1.00147.88 O ATOM 2498 O5 NAG B1501 -6.475 54.975 13.813 1.00140.98 O ATOM 2499 O6 NAG B1501 -3.393 55.387 13.064 1.00142.01 O ATOM 2500 O7 NAG B1501 -11.324 56.202 14.824 1.00148.00 O ATOM 2501 C1 GLC A1502 -15.185 22.024 26.056 1.00110.36 C ATOM 2502 C2 GLC A1502 -16.471 21.825 26.845 1.00113.20 C ATOM 2503 C3 GLC A1502 -16.211 22.001 28.346 1.00114.91 C ATOM 2504 C4 GLC A1502 -15.029 21.128 28.831 1.00114.73 C ATOM 2505 C5 GLC A1502 -13.844 21.292 27.845 1.00111.77 C ATOM 2506 C6 GLC A1502 -12.639 20.389 28.083 1.00111.66 C ATOM 2507 C7 GLC A1502 -18.403 22.364 25.475 1.00114.13 C ATOM 2508 C8 GLC A1502 -19.807 22.241 26.012 1.00117.31 C ATOM 2509 O GLC A1502 -14.242 21.080 26.507 1.00110.44 O ATOM 2510 O3 GLC A1502 -17.405 21.776 29.080 1.00117.91 O ATOM 2511 O4 GLC A1502 -14.600 21.510 30.140 1.00116.15 O ATOM 2512 O6 GLC A1502 -13.060 19.359 28.928 1.00114.27 O ATOM 2513 O7 GLC A1502 -18.154 22.117 24.281 1.00112.49 O ATOM 2514 N2 GLC A1502 -17.478 22.750 26.363 1.00113.56 N END end end write coordinates format=pdbo end ! now test error handing for applying patch residues set abort=off end patch nuc refer=-=( resid 1 ) refe=+=( resid 2 ) end end set message=normal end patch nuc refer=-=( resid 1 ) refe=+=( resid 2 ) end end stop