remarks XPACK.INP remarks test the crystallographic packing facility parameter @TOPPAR:param19.pro end {* read a ca trace *} struc PSF 6 !NTITLE REMARKS FILENAME="TH:[BRUNGER.XREFIN.LACTAL]JUNK.PSF;1" REMARKS - parameter file PARAM19 - REMARKS PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) REMARKS TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) REMARKS JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 REMARKS DATE: 8-SEP-86 14:23:44 created by user: BRUNGER 123 !NATOM 1 1 LYS CA CH1E 0.250000 13.0190 0 2 2 GLN CA CH1E 0.100000 13.0190 0 3 3 PHE CA CH1E 0.100000 13.0190 0 4 4 THR CA CH1E 0.100000 13.0190 0 5 5 LYS CA CH1E 0.100000 13.0190 0 6 6 CYS CA CH1E 0.100000 13.0190 0 7 7 GLU CA CH1E 0.100000 13.0190 0 8 8 LEU CA CH1E 0.100000 13.0190 0 9 9 SER CA CH1E 0.100000 13.0190 0 10 10 GLN CA CH1E 0.100000 13.0190 0 11 11 LEU CA CH1E 0.100000 13.0190 0 12 12 LEU CA CH1E 0.100000 13.0190 0 13 13 LYS CA CH1E 0.100000 13.0190 0 14 14 ASP CA CH1E 0.100000 13.0190 0 15 15 ILE CA CH1E 0.100000 13.0190 0 16 16 ASP CA CH1E 0.100000 13.0190 0 17 17 GLY CA CH2E 0.100000 14.0270 0 18 18 TYR CA CH1E 0.100000 13.0190 0 19 19 GLY CA CH2E 0.100000 14.0270 0 20 20 GLY CA CH2E 0.100000 14.0270 0 21 21 ILE CA CH1E 0.100000 13.0190 0 22 22 ALA CA CH1E 0.100000 13.0190 0 23 23 LEU CA CH1E 0.100000 13.0190 0 24 24 PRO CA CH1E 0.100000 13.0190 0 25 25 GLU CA CH1E 0.100000 13.0190 0 26 26 LEU CA CH1E 0.100000 13.0190 0 27 27 ILE CA CH1E 0.100000 13.0190 0 28 28 CYS CA CH1E 0.100000 13.0190 0 29 29 THR CA CH1E 0.100000 13.0190 0 30 30 MET CA CH1E 0.100000 13.0190 0 31 31 PHE CA CH1E 0.100000 13.0190 0 32 32 HIS CA CH1E 0.100000 13.0190 0 33 33 THR CA CH1E 0.100000 13.0190 0 34 34 SER CA CH1E 0.100000 13.0190 0 35 35 GLY CA CH2E 0.100000 14.0270 0 36 36 TYR CA CH1E 0.100000 13.0190 0 37 37 ASP CA CH1E 0.100000 13.0190 0 38 38 THR CA CH1E 0.100000 13.0190 0 39 39 GLN CA CH1E 0.100000 13.0190 0 40 40 ALA CA CH1E 0.100000 13.0190 0 41 41 ILE CA CH1E 0.100000 13.0190 0 42 42 VAL CA CH1E 0.100000 13.0190 0 43 43 GLU CA CH1E 0.100000 13.0190 0 44 44 ASN CA CH1E 0.100000 13.0190 0 45 45 ASN CA CH1E 0.100000 13.0190 0 46 46 GLU CA CH1E 0.100000 13.0190 0 47 47 SER CA CH1E 0.100000 13.0190 0 48 48 THR CA CH1E 0.100000 13.0190 0 49 49 GLU CA CH1E 0.100000 13.0190 0 50 50 TYR CA CH1E 0.100000 13.0190 0 51 51 GLY CA CH2E 0.100000 14.0270 0 52 52 LEU CA CH1E 0.100000 13.0190 0 53 53 PHE CA CH1E 0.100000 13.0190 0 54 54 GLN CA CH1E 0.100000 13.0190 0 55 55 ILE CA CH1E 0.100000 13.0190 0 56 56 SER CA CH1E 0.100000 13.0190 0 57 57 ASN CA CH1E 0.100000 13.0190 0 58 58 LYS CA CH1E 0.100000 13.0190 0 59 59 LEU CA CH1E 0.100000 13.0190 0 60 60 TRP CA CH1E 0.100000 13.0190 0 61 61 CYS CA CH1E 0.100000 13.0190 0 62 62 LYS CA CH1E 0.100000 13.0190 0 63 63 SER CA CH1E 0.100000 13.0190 0 64 64 SER CA CH1E 0.100000 13.0190 0 65 65 GLN CA CH1E 0.100000 13.0190 0 66 66 VAL CA CH1E 0.100000 13.0190 0 67 67 PRO CA CH1E 0.100000 13.0190 0 68 68 GLN CA CH1E 0.100000 13.0190 0 69 69 SER CA CH1E 0.100000 13.0190 0 70 70 ARG CA CH1E 0.100000 13.0190 0 71 71 ASN CA CH1E 0.100000 13.0190 0 72 72 ILE CA CH1E 0.100000 13.0190 0 73 73 CYS CA CH1E 0.100000 13.0190 0 74 74 ASP CA CH1E 0.100000 13.0190 0 75 75 ILE CA CH1E 0.100000 13.0190 0 76 76 SER CA CH1E 0.100000 13.0190 0 77 77 CYS CA CH1E 0.100000 13.0190 0 78 78 ASP CA CH1E 0.100000 13.0190 0 79 79 LYS CA CH1E 0.100000 13.0190 0 80 80 PHE CA CH1E 0.100000 13.0190 0 81 81 LEU CA CH1E 0.100000 13.0190 0 82 82 ASP CA CH1E 0.100000 13.0190 0 83 83 ASP CA CH1E 0.100000 13.0190 0 84 84 ASP CA CH1E 0.100000 13.0190 0 85 85 ILE CA CH1E 0.100000 13.0190 0 86 86 THR CA CH1E 0.100000 13.0190 0 87 87 ASP CA CH1E 0.100000 13.0190 0 88 88 ASP CA CH1E 0.100000 13.0190 0 89 89 ILE CA CH1E 0.100000 13.0190 0 90 90 MET CA CH1E 0.100000 13.0190 0 91 91 CYS CA CH1E 0.100000 13.0190 0 92 92 ALA CA CH1E 0.100000 13.0190 0 93 93 LYS CA CH1E 0.100000 13.0190 0 94 94 LYS CA CH1E 0.100000 13.0190 0 95 95 ILE CA CH1E 0.100000 13.0190 0 96 96 LEU CA CH1E 0.100000 13.0190 0 97 97 ASP CA CH1E 0.100000 13.0190 0 98 98 ILE CA CH1E 0.100000 13.0190 0 99 99 LYS CA CH1E 0.100000 13.0190 0 100 100 GLY CA CH2E 0.100000 14.0270 0 101 101 ILE CA CH1E 0.100000 13.0190 0 102 102 ASP CA CH1E 0.100000 13.0190 0 103 103 TYR CA CH1E 0.100000 13.0190 0 104 104 TRP CA CH1E 0.100000 13.0190 0 105 105 LEU CA CH1E 0.100000 13.0190 0 106 106 ALA CA CH1E 0.100000 13.0190 0 107 107 HIS CA CH1E 0.100000 13.0190 0 108 108 LYS CA CH1E 0.100000 13.0190 0 109 109 ALA CA CH1E 0.100000 13.0190 0 110 110 LEU CA CH1E 0.100000 13.0190 0 111 111 CYS CA CH1E 0.100000 13.0190 0 112 112 THR CA CH1E 0.100000 13.0190 0 113 113 GLU CA CH1E 0.100000 13.0190 0 114 114 LYS CA CH1E 0.100000 13.0190 0 115 115 LEU CA CH1E 0.100000 13.0190 0 116 116 GLU CA CH1E 0.100000 13.0190 0 117 117 GLN CA CH1E 0.100000 13.0190 0 118 118 TRP CA CH1E 0.100000 13.0190 0 119 119 LEU CA CH1E 0.100000 13.0190 0 120 120 CYS CA CH1E 0.100000 13.0190 0 121 121 GLU CA CH1E 0.100000 13.0190 0 122 122 LYS CA CH1E 0.100000 13.0190 0 123 123 LEU CA CH1E 0.100000 13.0190 0 0 !NBOND: bonds 0 !NTHETA: angles 0 !NPHI: dihedrals 0 !NIMPHI: impropers 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 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 0 0 0 0 123 0 !NGRP 0 2 0 1 2 0 2 2 0 3 2 0 4 2 0 5 2 0 6 2 0 7 2 0 8 2 0 9 2 0 10 2 0 11 2 0 12 2 0 13 2 0 14 2 0 15 2 0 16 2 0 17 2 0 18 2 0 19 2 0 20 2 0 21 2 0 22 2 0 23 2 0 24 2 0 25 2 0 26 2 0 27 2 0 28 2 0 29 2 0 30 2 0 31 2 0 32 2 0 33 2 0 34 2 0 35 2 0 36 2 0 37 2 0 38 2 0 39 2 0 40 2 0 41 2 0 42 2 0 43 2 0 44 2 0 45 2 0 46 2 0 47 2 0 48 2 0 49 2 0 50 2 0 51 2 0 52 2 0 53 2 0 54 2 0 55 2 0 56 2 0 57 2 0 58 2 0 59 2 0 60 2 0 61 2 0 62 2 0 63 2 0 64 2 0 65 2 0 66 2 0 67 2 0 68 2 0 69 2 0 70 2 0 71 2 0 72 2 0 73 2 0 74 2 0 75 2 0 76 2 0 77 2 0 78 2 0 79 2 0 80 2 0 81 2 0 82 2 0 83 2 0 84 2 0 85 2 0 86 2 0 87 2 0 88 2 0 89 2 0 90 2 0 91 2 0 92 2 0 93 2 0 94 2 0 95 2 0 96 2 0 97 2 0 98 2 0 99 2 0 100 2 0 101 2 0 102 2 0 103 2 0 104 2 0 105 2 0 106 2 0 107 2 0 108 2 0 109 2 0 110 2 0 111 2 0 112 2 0 113 2 0 114 2 0 115 2 0 116 2 0 117 2 0 118 2 0 119 2 0 120 2 0 121 2 0 122 2 0 end coor REMARK FILENAME="TH:[BRUNGER.XREFIN.LACTAL]JUNK.PDB;1" REMARK - parameter file PARAM19 - REMARK PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) REMARK TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) REMARK JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 REMARK DATE: 8-SEP-86 14:23:36 created by user: BRUNGER ATOM 1 CA LYS 1 7.781 27.092 15.335 0.00 12.00 ATOM 2 CA GLN 2 8.641 26.707 11.942 0.00 12.00 ATOM 3 CA PHE 3 11.898 28.359 10.550 0.00 12.00 ATOM 4 CA THR 4 13.634 30.109 7.535 0.00 12.00 ATOM 5 CA LYS 5 15.403 26.982 6.209 0.00 12.00 ATOM 6 CA CYS 6 18.644 28.776 7.415 0.00 12.00 ATOM 7 CA GLU 7 18.999 28.489 11.108 0.00 12.00 ATOM 8 CA LEU 8 17.849 25.008 10.534 0.00 12.00 ATOM 9 CA SER 9 21.181 25.164 8.586 0.00 12.00 ATOM 10 CA GLN 10 23.379 26.866 11.224 0.00 12.00 ATOM 11 CA LEU 11 21.773 24.849 14.222 0.00 12.00 ATOM 12 CA LEU 12 22.318 21.705 12.129 0.00 12.00 ATOM 13 CA LYS 13 25.914 21.819 10.462 0.00 12.00 ATOM 14 CA ASP 14 26.729 19.567 13.461 0.00 12.00 ATOM 15 CA ILE 15 24.715 16.642 12.345 0.00 12.00 ATOM 16 CA ASP 16 25.365 15.950 8.674 0.00 12.00 ATOM 17 CA GLY 17 27.821 13.431 7.429 0.00 12.00 ATOM 18 CA TYR 18 28.327 10.841 9.869 0.00 12.00 ATOM 19 CA GLY 19 25.109 9.042 10.357 0.00 12.00 ATOM 20 CA GLY 20 25.811 7.474 7.062 0.00 12.00 ATOM 21 CA ILE 21 23.667 10.281 6.020 0.00 12.00 ATOM 22 CA ALA 22 24.683 13.766 4.722 0.00 12.00 ATOM 23 CA LEU 23 22.865 17.195 4.870 0.00 12.00 ATOM 24 CA PRO 24 20.480 17.725 2.811 0.00 12.00 ATOM 25 CA GLU 25 18.860 14.438 2.320 0.00 12.00 ATOM 26 CA LEU 26 17.932 15.488 6.077 0.00 12.00 ATOM 27 CA ILE 27 17.194 18.994 4.844 0.00 12.00 ATOM 28 CA CYS 28 14.583 17.598 2.368 0.00 12.00 ATOM 29 CA THR 29 12.856 15.480 5.080 0.00 12.00 ATOM 30 CA MET 30 13.102 18.570 7.148 0.00 12.00 ATOM 31 CA PHE 31 10.633 19.991 4.696 0.00 12.00 ATOM 32 CA HIS 32 8.926 16.804 3.817 0.00 12.00 ATOM 33 CA THR 33 8.084 14.992 7.064 0.00 12.00 ATOM 34 CA SER 34 5.740 17.455 8.390 0.00 12.00 ATOM 35 CA GLY 35 7.826 19.626 8.185 0.00 12.00 ATOM 36 CA TYR 36 9.980 21.715 10.374 0.00 12.00 ATOM 37 CA ASP 37 7.407 23.172 12.792 0.00 12.00 ATOM 38 CA THR 38 8.069 22.085 16.410 0.00 12.00 ATOM 39 CA GLN 39 4.630 21.899 17.697 0.00 12.00 ATOM 40 CA ALA 40 3.908 19.490 14.729 0.00 12.00 ATOM 41 CA ILE 41 2.106 16.493 16.272 0.00 12.00 ATOM 42 CA VAL 42 0.094 13.911 14.382 0.00 12.00 ATOM 43 CA GLU 43 -1.459 10.414 15.028 0.00 12.00 ATOM 44 CA ASN 44 0.377 8.201 12.496 0.00 12.00 ATOM 45 CA ASN 45 -1.721 5.485 12.390 0.00 12.00 ATOM 46 CA GLU 46 -2.471 4.746 16.078 0.00 12.00 ATOM 47 CA SER 47 0.813 5.829 17.727 0.00 12.00 ATOM 48 CA THR 48 1.557 9.509 16.962 0.00 12.00 ATOM 49 CA GLU 49 4.586 11.507 15.715 0.00 12.00 ATOM 50 CA TYR 50 5.432 14.542 17.810 0.00 12.00 ATOM 51 CA GLY 51 7.807 17.183 16.652 0.00 12.00 ATOM 52 CA LEU 52 9.092 18.380 13.332 0.00 12.00 ATOM 53 CA PHE 53 8.259 15.092 11.913 0.00 12.00 ATOM 54 CA GLN 54 8.335 11.520 13.132 0.00 12.00 ATOM 55 CA ILE 55 10.127 10.601 16.210 0.00 12.00 ATOM 56 CA SER 56 7.984 8.809 18.089 0.00 12.00 ATOM 57 CA ASN 57 5.673 7.275 20.201 0.00 12.00 ATOM 58 CA LYS 58 5.379 3.582 20.494 0.00 12.00 ATOM 59 CA LEU 59 9.110 3.553 20.749 0.00 12.00 ATOM 60 CA TRP 60 11.684 6.208 21.596 0.00 12.00 ATOM 61 CA CYS 61 9.479 8.391 23.775 0.00 12.00 ATOM 62 CA LYS 62 6.862 8.300 26.813 0.00 12.00 ATOM 63 CA SER 63 3.081 9.227 26.699 0.00 12.00 ATOM 64 CA SER 64 -0.114 7.223 26.937 0.00 12.00 ATOM 65 CA GLN 65 0.573 4.799 24.244 0.00 12.00 ATOM 66 CA VAL 66 2.117 2.322 26.810 0.00 12.00 ATOM 67 CA PRO 67 2.940 -0.637 26.441 0.00 12.00 ATOM 68 CA GLN 68 5.071 -1.459 24.332 0.00 12.00 ATOM 69 CA SER 69 7.667 1.376 24.429 0.00 12.00 ATOM 70 CA ARG 70 11.465 0.827 24.203 0.00 12.00 ATOM 71 CA ASN 71 12.169 4.367 25.357 0.00 12.00 ATOM 72 CA ILE 72 15.632 4.272 23.657 0.00 12.00 ATOM 73 CA CYS 73 16.025 7.954 24.364 0.00 12.00 ATOM 74 CA ASP 74 15.038 8.970 27.911 0.00 12.00 ATOM 75 CA ILE 75 12.243 11.056 26.730 0.00 12.00 ATOM 76 CA SER 76 9.116 12.852 27.475 0.00 12.00 ATOM 77 CA CYS 77 6.940 13.654 24.438 0.00 12.00 ATOM 78 CA ASP 78 6.799 16.978 26.286 0.00 12.00 ATOM 79 CA LYS 79 10.478 17.863 25.625 0.00 12.00 ATOM 80 CA PHE 80 9.152 16.332 22.473 0.00 12.00 ATOM 81 CA LEU 81 6.768 19.201 22.057 0.00 12.00 ATOM 82 CA ASP 82 8.418 22.554 21.060 0.00 12.00 ATOM 83 CA ASP 83 11.532 24.868 22.016 0.00 12.00 ATOM 84 CA ASP 84 15.150 24.037 23.090 0.00 12.00 ATOM 85 CA ILE 85 15.564 21.728 20.101 0.00 12.00 ATOM 86 CA THR 86 19.253 21.393 20.470 0.00 12.00 ATOM 87 CA ASP 87 18.510 18.513 22.781 0.00 12.00 ATOM 88 CA ASP 88 16.658 16.292 21.613 0.00 12.00 ATOM 89 CA ILE 89 18.130 16.144 18.499 0.00 12.00 ATOM 90 CA MET 90 20.371 13.857 20.305 0.00 12.00 ATOM 91 CA CYS 91 17.379 11.608 20.039 0.00 12.00 ATOM 92 CA ALA 92 17.341 11.966 16.241 0.00 12.00 ATOM 93 CA LYS 93 20.918 10.482 16.503 0.00 12.00 ATOM 94 CA LYS 94 19.853 7.649 19.086 0.00 12.00 ATOM 95 CA ILE 95 17.470 6.111 16.306 0.00 12.00 ATOM 96 CA LEU 96 20.264 6.624 13.796 0.00 12.00 ATOM 97 CA ASP 97 22.940 5.100 15.701 0.00 12.00 ATOM 98 CA ILE 98 20.319 2.303 15.079 0.00 12.00 ATOM 99 CA LYS 99 18.905 2.890 11.464 0.00 12.00 ATOM 100 CA GLY 100 18.693 6.474 10.492 0.00 12.00 ATOM 101 CA ILE 101 18.061 8.141 8.030 0.00 12.00 ATOM 102 CA ASP 102 15.931 5.570 6.053 0.00 12.00 ATOM 103 CA TYR 103 13.812 5.250 9.136 0.00 12.00 ATOM 104 CA TRP 104 12.018 8.334 7.548 0.00 12.00 ATOM 105 CA LEU 105 8.929 8.296 5.259 0.00 12.00 ATOM 106 CA ALA 106 10.009 10.671 2.409 0.00 12.00 ATOM 107 CA HIS 107 13.689 10.019 2.166 0.00 12.00 ATOM 108 CA LYS 108 14.178 7.031 0.329 0.00 12.00 ATOM 109 CA ALA 109 14.684 8.411 -3.131 0.00 12.00 ATOM 110 CA LEU 110 12.808 11.906 -2.787 0.00 12.00 ATOM 111 CA CYS 111 16.174 13.041 -1.157 0.00 12.00 ATOM 112 CA THR 112 19.342 10.974 -2.046 0.00 12.00 ATOM 113 CA GLU 113 18.499 10.770 -5.270 0.00 12.00 ATOM 114 CA LYS 114 18.670 13.887 -5.515 0.00 12.00 ATOM 115 CA LEU 115 19.429 16.558 -8.102 0.00 12.00 ATOM 116 CA GLU 116 20.007 18.357 -5.015 0.00 12.00 ATOM 117 CA GLN 117 21.745 21.793 -5.168 0.00 12.00 ATOM 118 CA TRP 118 21.211 23.117 -1.974 0.00 12.00 ATOM 119 CA LEU 119 22.449 24.976 0.961 0.00 12.00 ATOM 120 CA CYS 120 21.917 28.743 2.280 0.00 12.00 ATOM 121 CA GLU 121 24.127 31.764 1.628 0.00 12.00 ATOM 122 CA LYS 122 26.314 32.982 3.604 0.00 12.00 ATOM 123 CA LEU 123 27.062 30.207 1.759 0.00 12.00 END {===================================================================} xrefin a=33.6 b=69.9 c=47.3 alpha=90.0 beta=90.0 gamma=90.0 {* space_group=P2(1)2(1)2 *} symmetry=(x,y,z) symmetry=(-x,-y,z) symmetry=(1/2+x,1/2-y,-z) symmetry=(1/2-x,1/2+y,-z) end parameter nbonds cutnb=7.0 wmin=0.5 ctonnb=5.0 ctofnb=6.0 end end flags exclude * include pvdw pele end distance cutoff=7.0 cuton=0.0 end distance cutoff=6. cuton=5.8 end test first sele=( resid 34 ) step=0.0002 tol=0.0 end {* now skew the unit-cell to test derivatives *} {* ========================================== *} xrefin alpha=60.0 beta=70.0 gamma=50.0 end distance cutoff=5.0 cuton=0.0 end test first sele=( resid 34 or resid 56 or resid 77 or resid 67 or resid 99 or resid 113 ) step=0.001 tol=0.0 end {* now we test the interaction criterium *} {* ===================================== *} cons interaction=( resid 99 )=( all ) end energy end display $pele display $pvdw cons interaction=( resid 99 )=( resid 96 ) end distance cutoff=7.0 cuton=0.0 end test first sele=( resid 99 or resid 96 ) step=0.001 tol=0.0 end {* test the automatic update business *} {* ================================== *} energy end coor translate sele=( resid 99 ) vector=( 0.0 0.4 0.0 ) end energy end coor translate sele=( resid 99 ) vector=( 0.0 0.2 0.0 ) end energy end flags incl vdw elec pvdw pele end cons inter=( resn t* ) ( prev ) end distance end stop end