remark This protocol allows computer to select dimer noes REMARKS very slow cooling with increase of vdw !this is from ubiquitint refinement !converting this to refine bax !---------------------------------------------------------------------- ! read in the PSF file and initial structure structure !@bax_short.psf PSF 18 !NTITLE REMARKS FILENAME="bax_short.psf" REMARKS =============================================================== REMARKS overall,bonds,angles,improper,vdw,noe,cdih,coup,dipo,dcsa REMARKS energies: 639.976,38.4998,250.39,35.5845,114.766,26.4132,1.18426,$COUP,173.138,$DCSA REMARKS =============================================================== REMARKS bonds,angles,impropers,noe REMARKS bonds etc: 3.575818E-03,0.549326,0.385884,3.252691E-02 REMARKS =============================================================== REMARKS noe REMARKS violations : 9 REMARKS =============================================================== REMARKS dipo dnh dnh2 dch dch2 dch3 dcc dcc2 REMARKS RMS dipo: 0 0 5.37589 1.44026 REMARKS 3.33263 1.31729 0.696583 REMARKS dcsa csa REMARKS RMS dcsa :0 REMARKS =============================================================== REMARKS DATE:05-Sep-02 11:39:46 created by user: rlipsitz 175 !NATOM 1 20 MET N NH1 -0.360000 14.0070 0 2 20 MET HN H 0.260000 1.00800 0 3 20 MET CA CT 0.000000E+00 12.0110 0 4 20 MET HA HA 0.100000 1.00800 0 5 20 MET CB CT -0.200000 12.0110 0 6 20 MET HB1 HA 0.100000 1.00800 0 7 20 MET HB2 HA 0.100000 1.00800 0 8 20 MET CG CT -0.115000 12.0110 0 9 20 MET HG1 HA 0.100000 1.00800 0 10 20 MET HG2 HA 0.100000 1.00800 0 11 20 MET SD S -0.170000 32.0600 0 12 20 MET CE CT -0.215000 12.0110 0 13 20 MET HE1 HA 0.100000 1.00800 0 14 20 MET HE2 HA 0.100000 1.00800 0 15 20 MET HE3 HA 0.100000 1.00800 0 16 20 MET C C 0.480000 12.0110 0 17 20 MET O O -0.480000 15.9990 0 18 21 LYS N NH1 -0.360000 14.0070 0 19 21 LYS HN H 0.260000 1.00800 0 20 21 LYS CA CT 0.000000E+00 12.0110 0 21 21 LYS HA HA 0.100000 1.00800 0 22 21 LYS CB CT -0.200000 12.0110 0 23 21 LYS HB1 HA 0.100000 1.00800 0 24 21 LYS HB2 HA 0.100000 1.00800 0 25 21 LYS CG CT -0.200000 12.0110 0 26 21 LYS HG1 HA 0.100000 1.00800 0 27 21 LYS HG2 HA 0.100000 1.00800 0 28 21 LYS CD CT -0.200000 12.0110 0 29 21 LYS HD1 HA 0.100000 1.00800 0 30 21 LYS HD2 HA 0.100000 1.00800 0 31 21 LYS CE CT 0.305000 12.0110 0 32 21 LYS HE1 HA 0.100000 1.00800 0 33 21 LYS HE2 HA 0.100000 1.00800 0 34 21 LYS NZ NH3 -0.810000 14.0070 0 35 21 LYS HZ1 HC 0.435000 1.00800 0 36 21 LYS HZ2 HC 0.435000 1.00800 0 37 21 LYS HZ3 HC 0.435000 1.00800 0 38 21 LYS C C 0.480000 12.0110 0 39 21 LYS O O -0.480000 15.9990 0 40 22 THR N NH1 -0.360000 14.0070 0 41 22 THR HN H 0.260000 1.00800 0 42 22 THR CA CT 0.000000E+00 12.0110 0 43 22 THR HA HA 0.100000 1.00800 0 44 22 THR CB CT 0.180000 12.0110 0 45 22 THR HB HA 0.100000 1.00800 0 46 22 THR OG1 OH -0.680000 15.9990 0 47 22 THR HG1 H 0.400000 1.00800 0 48 22 THR CG2 CT -0.300000 12.0110 0 49 22 THR HG21 HA 0.100000 1.00800 0 50 22 THR HG22 HA 0.100000 1.00800 0 51 22 THR HG23 HA 0.100000 1.00800 0 52 22 THR C C 0.480000 12.0110 0 53 22 THR O O -0.480000 15.9990 0 54 23 GLY N NH1 -0.360000 14.0070 0 55 23 GLY HN H 0.260000 1.00800 0 56 23 GLY CA CT -0.100000 12.0110 0 57 23 GLY HA1 HA 0.100000 1.00800 0 58 23 GLY HA2 HA 0.100000 1.00800 0 59 23 GLY C C 0.480000 12.0110 0 60 23 GLY O O -0.480000 15.9990 0 61 24 ALA N NH1 -0.360000 14.0070 0 62 24 ALA HN H 0.260000 1.00800 0 63 24 ALA CA CT 0.000000E+00 12.0110 0 64 24 ALA HA HA 0.100000 1.00800 0 65 24 ALA CB CT -0.300000 12.0110 0 66 24 ALA HB1 HA 0.100000 1.00800 0 67 24 ALA HB2 HA 0.100000 1.00800 0 68 24 ALA HB3 HA 0.100000 1.00800 0 69 24 ALA C C 0.480000 12.0110 0 70 24 ALA O O -0.480000 15.9990 0 71 25 LEU N NH1 -0.360000 14.0070 0 72 25 LEU HN H 0.260000 1.00800 0 73 25 LEU CA CT 0.000000E+00 12.0110 0 74 25 LEU HA HA 0.100000 1.00800 0 75 25 LEU CB CT -0.200000 12.0110 0 76 25 LEU HB1 HA 0.100000 1.00800 0 77 25 LEU HB2 HA 0.100000 1.00800 0 78 25 LEU CG CT -0.100000 12.0110 0 79 25 LEU HG HA 0.100000 1.00800 0 80 25 LEU CD1 CT -0.300000 12.0110 0 81 25 LEU HD11 HA 0.100000 1.00800 0 82 25 LEU HD12 HA 0.100000 1.00800 0 83 25 LEU HD13 HA 0.100000 1.00800 0 84 25 LEU CD2 CT -0.300000 12.0110 0 85 25 LEU HD21 HA 0.100000 1.00800 0 86 25 LEU HD22 HA 0.100000 1.00800 0 87 25 LEU HD23 HA 0.100000 1.00800 0 88 25 LEU C C 0.480000 12.0110 0 89 25 LEU O O -0.480000 15.9990 0 90 26 LEU N NH1 -0.360000 14.0070 0 91 26 LEU HN H 0.260000 1.00800 0 92 26 LEU CA CT 0.000000E+00 12.0110 0 93 26 LEU HA HA 0.100000 1.00800 0 94 26 LEU CB CT -0.200000 12.0110 0 95 26 LEU HB1 HA 0.100000 1.00800 0 96 26 LEU HB2 HA 0.100000 1.00800 0 97 26 LEU CG CT -0.100000 12.0110 0 98 26 LEU HG HA 0.100000 1.00800 0 99 26 LEU CD1 CT -0.300000 12.0110 0 100 26 LEU HD11 HA 0.100000 1.00800 0 101 26 LEU HD12 HA 0.100000 1.00800 0 102 26 LEU HD13 HA 0.100000 1.00800 0 103 26 LEU CD2 CT -0.300000 12.0110 0 104 26 LEU HD21 HA 0.100000 1.00800 0 105 26 LEU HD22 HA 0.100000 1.00800 0 106 26 LEU HD23 HA 0.100000 1.00800 0 107 26 LEU C C 0.480000 12.0110 0 108 26 LEU O O -0.480000 15.9990 0 109 27 LEU N NH1 -0.360000 14.0070 0 110 27 LEU HN H 0.260000 1.00800 0 111 27 LEU CA CT 0.000000E+00 12.0110 0 112 27 LEU HA HA 0.100000 1.00800 0 113 27 LEU CB CT -0.200000 12.0110 0 114 27 LEU HB1 HA 0.100000 1.00800 0 115 27 LEU HB2 HA 0.100000 1.00800 0 116 27 LEU CG CT -0.100000 12.0110 0 117 27 LEU HG HA 0.100000 1.00800 0 118 27 LEU CD1 CT -0.300000 12.0110 0 119 27 LEU HD11 HA 0.100000 1.00800 0 120 27 LEU HD12 HA 0.100000 1.00800 0 121 27 LEU HD13 HA 0.100000 1.00800 0 122 27 LEU CD2 CT -0.300000 12.0110 0 123 27 LEU HD21 HA 0.100000 1.00800 0 124 27 LEU HD22 HA 0.100000 1.00800 0 125 27 LEU HD23 HA 0.100000 1.00800 0 126 27 LEU C C 0.480000 12.0110 0 127 27 LEU O O -0.480000 15.9990 0 128 28 GLN N NH1 -0.360000 14.0070 0 129 28 GLN HN H 0.260000 1.00800 0 130 28 GLN CA CT 0.000000E+00 12.0110 0 131 28 GLN HA HA 0.100000 1.00800 0 132 28 GLN CB CT -0.200000 12.0110 0 133 28 GLN HB1 HA 0.100000 1.00800 0 134 28 GLN HB2 HA 0.100000 1.00800 0 135 28 GLN CG CT -0.200000 12.0110 0 136 28 GLN HG1 HA 0.100000 1.00800 0 137 28 GLN HG2 HA 0.100000 1.00800 0 138 28 GLN CD C 0.480000 12.0110 0 139 28 GLN OE1 O -0.480000 15.9990 0 140 28 GLN NE2 NH2 -0.520000 14.0070 0 141 28 GLN HE21 H 0.260000 1.00800 0 142 28 GLN HE22 H 0.260000 1.00800 0 143 28 GLN C C 0.480000 12.0110 0 144 28 GLN O O -0.480000 15.9990 0 145 29 GLY N NH1 -0.360000 14.0070 0 146 29 GLY HN H 0.260000 1.00800 0 147 29 GLY CA CT -0.100000 12.0110 0 148 29 GLY HA1 HA 0.100000 1.00800 0 149 29 GLY HA2 HA 0.100000 1.00800 0 150 29 GLY C C 0.480000 12.0110 0 151 29 GLY O O -0.480000 15.9990 0 152 30 PHE N NH1 -0.360000 14.0070 0 153 30 PHE HN H 0.260000 1.00800 0 154 30 PHE CA CT 0.000000E+00 12.0110 0 155 30 PHE HA HA 0.100000 1.00800 0 156 30 PHE CB CT -0.160000 12.0110 0 157 30 PHE HB1 HA 0.100000 1.00800 0 158 30 PHE HB2 HA 0.100000 1.00800 0 159 30 PHE CG CA 0.300000E-01 12.0110 0 160 30 PHE CD1 CA -0.160000 12.0110 0 161 30 PHE HD1 HA 0.140000 1.00800 0 162 30 PHE CD2 CA -0.160000 12.0110 0 163 30 PHE HD2 HA 0.140000 1.00800 0 164 30 PHE CE1 CA -0.150000 12.0110 0 165 30 PHE HE1 HA 0.140000 1.00800 0 166 30 PHE CE2 CA -0.150000 12.0110 0 167 30 PHE HE2 HA 0.140000 1.00800 0 168 30 PHE CZ CA -0.150000 12.0110 0 169 30 PHE HZ HA 0.140000 1.00800 0 170 30 PHE C C 0.480000 12.0110 0 171 30 PHE O O -0.480000 15.9990 0 172 500 ANI X XXX 0.000000E+00 10.0000 0 173 500 ANI Y YYY 0.000000E+00 10.0000 0 174 500 ANI Z ZZZ 0.000000E+00 10.0000 0 175 500 ANI OO OOO 0.000000E+00 10.0000 0 174 !NBOND: bonds 1 2 1 3 3 4 3 5 5 6 5 7 5 8 8 9 8 10 8 11 11 12 12 13 12 14 12 15 3 16 16 17 18 19 18 20 20 21 20 22 22 23 22 24 22 25 25 26 25 27 25 28 28 29 28 30 28 31 31 32 31 33 31 34 34 35 34 36 34 37 20 38 38 39 16 18 40 41 40 42 42 43 42 44 44 45 44 46 46 47 44 48 48 49 48 50 48 51 42 52 52 53 38 40 54 55 54 56 56 57 56 58 56 59 59 60 52 54 61 62 61 63 63 64 63 65 65 66 65 67 65 68 63 69 69 70 59 61 71 72 71 73 73 74 73 75 75 76 75 77 75 78 78 79 78 80 80 81 80 82 80 83 78 84 84 85 84 86 84 87 73 88 88 89 69 71 90 91 90 92 92 93 92 94 94 95 94 96 94 97 97 98 97 99 99 100 99 101 99 102 97 103 103 104 103 105 103 106 92 107 107 108 88 90 109 110 109 111 111 112 111 113 113 114 113 115 113 116 116 117 116 118 118 119 118 120 118 121 116 122 122 123 122 124 122 125 111 126 126 127 107 109 128 129 128 130 130 131 130 132 132 133 132 134 132 135 135 136 135 137 135 138 138 139 138 140 140 141 140 142 130 143 143 144 126 128 145 146 145 147 147 148 147 149 147 150 150 151 143 145 152 153 152 154 154 155 154 156 156 157 156 158 156 159 159 160 160 161 159 162 162 163 160 164 164 165 162 166 166 167 164 168 168 169 166 168 154 170 170 171 150 152 175 172 175 173 175 174 313 !NTHETA: angles 2 1 3 1 3 4 1 3 5 1 3 16 4 3 5 4 3 16 3 5 6 3 5 7 3 5 8 5 3 16 6 5 7 6 5 8 7 5 8 5 8 9 5 8 10 5 8 11 9 8 10 9 8 11 10 8 11 8 11 12 11 12 13 11 12 14 11 12 15 13 12 14 13 12 15 14 12 15 3 16 17 19 18 20 18 20 21 18 20 22 18 20 38 21 20 22 21 20 38 20 22 23 20 22 24 20 22 25 22 20 38 23 22 24 23 22 25 24 22 25 22 25 26 22 25 27 22 25 28 26 25 27 26 25 28 27 25 28 25 28 29 25 28 30 25 28 31 29 28 30 29 28 31 30 28 31 28 31 32 28 31 33 28 31 34 32 31 33 32 31 34 33 31 34 31 34 35 31 34 36 31 34 37 35 34 36 35 34 37 36 34 37 20 38 39 3 16 18 17 16 18 16 18 20 16 18 19 41 40 42 40 42 43 40 42 44 40 42 52 43 42 44 43 42 52 42 44 45 42 44 46 42 44 48 44 42 52 45 44 46 45 44 48 44 46 47 46 44 48 44 48 49 44 48 50 44 48 51 49 48 50 49 48 51 50 48 51 42 52 53 20 38 40 39 38 40 38 40 42 38 40 41 55 54 56 54 56 57 54 56 58 54 56 59 57 56 58 57 56 59 58 56 59 56 59 60 42 52 54 53 52 54 52 54 56 52 54 55 62 61 63 61 63 64 61 63 65 61 63 69 64 63 65 64 63 69 63 65 66 63 65 67 63 65 68 65 63 69 66 65 67 66 65 68 67 65 68 63 69 70 56 59 61 60 59 61 59 61 63 59 61 62 72 71 73 71 73 74 71 73 75 71 73 88 74 73 75 74 73 88 73 75 76 73 75 77 73 75 78 75 73 88 76 75 77 76 75 78 77 75 78 75 78 79 75 78 80 75 78 84 79 78 80 79 78 84 78 80 81 78 80 82 78 80 83 80 78 84 81 80 82 81 80 83 82 80 83 78 84 85 78 84 86 78 84 87 85 84 86 85 84 87 86 84 87 73 88 89 63 69 71 70 69 71 69 71 73 69 71 72 91 90 92 90 92 93 90 92 94 90 92 107 93 92 94 93 92 107 92 94 95 92 94 96 92 94 97 94 92 107 95 94 96 95 94 97 96 94 97 94 97 98 94 97 99 94 97 103 98 97 99 98 97 103 97 99 100 97 99 101 97 99 102 99 97 103 100 99 101 100 99 102 101 99 102 97 103 104 97 103 105 97 103 106 104 103 105 104 103 106 105 103 106 92 107 108 73 88 90 89 88 90 88 90 92 88 90 91 110 109 111 109 111 112 109 111 113 109 111 126 112 111 113 112 111 126 111 113 114 111 113 115 111 113 116 113 111 126 114 113 115 114 113 116 115 113 116 113 116 117 113 116 118 113 116 122 117 116 118 117 116 122 116 118 119 116 118 120 116 118 121 118 116 122 119 118 120 119 118 121 120 118 121 116 122 123 116 122 124 116 122 125 123 122 124 123 122 125 124 122 125 111 126 127 92 107 109 108 107 109 107 109 111 107 109 110 129 128 130 128 130 131 128 130 132 128 130 143 131 130 132 131 130 143 130 132 133 130 132 134 130 132 135 132 130 143 133 132 134 133 132 135 134 132 135 132 135 136 132 135 137 132 135 138 136 135 137 136 135 138 137 135 138 135 138 139 135 138 140 139 138 140 138 140 141 138 140 142 141 140 142 130 143 144 111 126 128 127 126 128 126 128 130 126 128 129 146 145 147 145 147 148 145 147 149 145 147 150 148 147 149 148 147 150 149 147 150 147 150 151 130 143 145 144 143 145 143 145 147 143 145 146 153 152 154 152 154 155 152 154 156 152 154 170 155 154 156 155 154 170 154 156 157 154 156 158 154 156 159 156 154 170 157 156 158 157 156 159 158 156 159 156 159 160 156 159 162 159 160 161 160 159 162 159 160 164 161 160 164 159 162 163 159 162 166 163 162 166 160 164 165 160 164 168 165 164 168 162 166 167 162 166 168 167 166 168 164 168 169 164 168 166 169 168 166 154 170 171 147 150 152 151 150 152 150 152 154 150 152 153 172 175 173 172 175 174 173 175 174 19 !NPHI: dihedrals 8 5 3 1 11 8 5 3 12 11 8 5 25 22 20 18 28 25 22 20 31 28 25 22 34 31 28 25 46 44 42 40 78 75 73 71 80 78 75 73 97 94 92 90 99 97 94 92 116 113 111 109 118 116 113 111 135 132 130 128 138 135 132 130 139 138 135 132 159 156 154 152 160 159 156 154 82 !NIMPHI: impropers 4 1 16 5 6 7 3 8 9 10 5 11 13 14 11 15 21 18 38 22 23 24 20 25 26 27 22 28 29 30 25 31 32 33 28 34 35 36 31 37 17 16 18 20 19 18 16 3 3 16 18 20 43 40 52 44 45 42 46 48 49 50 44 51 39 38 40 42 41 40 38 20 20 38 40 42 57 58 54 59 53 52 54 56 55 54 52 42 42 52 54 56 64 61 69 65 66 67 63 68 60 59 61 63 62 61 59 56 56 59 61 63 74 71 88 75 79 75 80 84 76 77 73 78 81 82 78 83 85 86 78 87 70 69 71 73 72 71 69 63 63 69 71 73 93 90 107 94 98 94 99 103 95 96 92 97 100 101 97 102 104 105 97 106 89 88 90 92 91 90 88 73 73 88 90 92 112 109 126 113 117 113 118 122 114 115 111 116 119 120 116 121 123 124 116 125 108 107 109 111 110 109 107 92 92 107 109 111 131 128 143 132 138 135 139 140 140 138 141 142 135 138 140 141 133 134 130 135 136 137 132 138 127 126 128 130 129 128 126 111 111 126 128 130 148 149 145 150 144 143 145 147 146 145 143 130 130 143 145 147 155 152 170 156 157 158 154 159 163 162 166 168 167 166 168 164 169 168 164 160 165 164 160 159 161 160 159 162 156 159 162 166 159 160 164 168 160 164 168 166 164 168 166 162 168 166 162 159 166 162 159 160 162 159 160 164 151 150 152 154 153 152 150 147 147 150 152 154 0 !NDON: donors 0 !NACC: acceptors 78 !NNB 85 86 87 79 85 86 87 79 85 86 87 79 81 82 83 79 81 82 83 79 81 82 83 79 104 105 106 98 104 105 106 98 104 105 106 98 100 101 102 98 100 101 102 98 100 101 102 98 123 124 125 117 123 124 125 117 123 124 125 117 119 120 121 117 119 120 121 117 119 120 121 117 168 166 164 162 160 159 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 4 8 12 12 16 20 24 24 24 24 24 24 24 24 24 24 24 24 24 28 32 36 36 40 44 48 48 48 48 48 48 48 48 48 48 48 48 48 52 56 60 60 64 68 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 72 73 74 74 75 75 76 76 77 77 78 78 78 78 78 78 78 78 70 0 !NGRP 0 0 0 2 0 0 4 0 0 7 0 0 10 0 0 11 0 0 15 0 0 17 0 0 19 0 0 21 0 0 24 0 0 27 0 0 30 0 0 33 0 0 37 0 0 39 0 0 41 0 0 43 0 0 45 0 0 47 0 0 51 0 0 53 0 0 55 0 0 58 0 0 60 0 0 62 0 0 64 0 0 68 0 0 70 0 0 72 0 0 74 0 0 77 0 0 79 0 0 83 0 0 87 0 0 89 0 0 91 0 0 93 0 0 96 0 0 98 0 0 102 0 0 106 0 0 108 0 0 110 0 0 112 0 0 115 0 0 117 0 0 121 0 0 125 0 0 127 0 0 129 0 0 131 0 0 134 0 0 137 0 0 139 0 0 142 0 0 144 0 0 146 0 0 149 0 0 151 0 0 153 0 0 155 0 0 158 0 0 159 0 0 161 0 0 163 0 0 165 0 0 167 0 0 169 0 0 171 0 0 end param @TOPPAR:parallhdg_new.pro @TOPPAR:par_axis.pro end coor !@bax_short.pdb REMARK FILENAME="bax_short.pdb" REMARK =============================================================== REMARK overall,bonds,angles,improper,vdw,noe,cdih,coup,dipo,dcsa REMARK energies: 639.976,38.4998,250.39,35.5845,114.766,26.4132,1.18426,$COUP,173.138,$DCSA REMARK =============================================================== REMARK bonds,angles,impropers,noe REMARK bonds etc: 3.575818E-03,0.549326,0.385884,3.252691E-02 REMARK =============================================================== REMARK noe REMARK violations : 9 REMARK =============================================================== REMARK dipo dnh dnh2 dch dch2 dch3 dcc dcc2 REMARK RMS dipo: 0 0 5.37589 1.44026 REMARK 3.33263 1.31729 0.696583 REMARK dcsa csa REMARK RMS dcsa :0 REMARK =============================================================== REMARK DATE:05-Sep-02 11:39:46 created by user: rlipsitz ATOM 1 N MET 20 10.802 6.788 -2.757 1.00 0.51 ATOM 2 HN MET 20 11.734 6.732 -2.459 1.00 0.57 ATOM 3 CA MET 20 9.999 8.005 -2.460 1.00 0.60 ATOM 4 HA MET 20 9.228 7.767 -1.742 1.00 0.71 ATOM 5 CB MET 20 10.920 9.085 -1.872 1.00 0.82 ATOM 6 HB1 MET 20 10.356 9.995 -1.738 1.00 1.15 ATOM 7 HB2 MET 20 11.730 9.270 -2.565 1.00 0.95 ATOM 8 CG MET 20 11.495 8.620 -0.508 1.00 1.07 ATOM 9 HG1 MET 20 12.576 8.616 -0.553 1.00 1.72 ATOM 10 HG2 MET 20 11.151 7.621 -0.277 1.00 1.52 ATOM 11 SD MET 20 10.964 9.743 0.814 1.00 1.43 ATOM 12 CE MET 20 9.222 9.254 0.857 1.00 0.93 ATOM 13 HE1 MET 20 9.151 8.199 1.086 1.00 1.32 ATOM 14 HE2 MET 20 8.768 9.443 -0.102 1.00 1.36 ATOM 15 HE3 MET 20 8.707 9.827 1.615 1.00 1.55 ATOM 16 C MET 20 9.359 8.522 -3.750 1.00 0.55 ATOM 17 O MET 20 8.244 9.005 -3.750 1.00 0.59 ATOM 18 N LYS 21 10.056 8.425 -4.853 1.00 0.57 ATOM 19 HN LYS 21 10.954 8.032 -4.832 1.00 0.62 ATOM 20 CA LYS 21 9.486 8.913 -6.144 1.00 0.61 ATOM 21 HA LYS 21 8.858 9.772 -5.952 1.00 0.64 ATOM 22 CB LYS 21 10.625 9.315 -7.084 1.00 0.72 ATOM 23 HB1 LYS 21 10.213 9.699 -8.005 1.00 0.93 ATOM 24 HB2 LYS 21 11.238 8.451 -7.296 1.00 0.99 ATOM 25 CG LYS 21 11.478 10.397 -6.420 1.00 1.09 ATOM 26 HG1 LYS 21 11.869 10.024 -5.485 1.00 1.41 ATOM 27 HG2 LYS 21 10.870 11.270 -6.233 1.00 1.39 ATOM 28 CD LYS 21 12.639 10.770 -7.343 1.00 1.24 ATOM 29 HD1 LYS 21 12.250 11.155 -8.274 1.00 1.52 ATOM 30 HD2 LYS 21 13.239 9.893 -7.539 1.00 1.54 ATOM 31 CE LYS 21 13.503 11.840 -6.673 1.00 1.80 ATOM 32 HE1 LYS 21 13.869 11.467 -5.728 1.00 2.26 ATOM 33 HE2 LYS 21 12.910 12.727 -6.504 1.00 2.25 ATOM 34 NZ LYS 21 14.656 12.173 -7.556 1.00 2.40 ATOM 35 HZ1 LYS 21 15.162 12.995 -7.171 1.00 2.80 ATOM 36 HZ2 LYS 21 14.307 12.395 -8.511 1.00 2.67 ATOM 37 HZ3 LYS 21 15.303 11.361 -7.603 1.00 2.91 ATOM 38 C LYS 21 8.661 7.798 -6.792 1.00 0.53 ATOM 39 O LYS 21 7.486 7.955 -7.057 1.00 0.51 ATOM 40 N THR 22 9.272 6.672 -7.052 1.00 0.53 ATOM 41 HN THR 22 10.223 6.567 -6.832 1.00 0.56 ATOM 42 CA THR 22 8.527 5.546 -7.685 1.00 0.52 ATOM 43 HA THR 22 8.167 5.853 -8.656 1.00 0.57 ATOM 44 CB THR 22 9.464 4.346 -7.846 1.00 0.55 ATOM 45 HB THR 22 9.830 4.043 -6.877 1.00 0.52 ATOM 46 OG1 THR 22 10.559 4.711 -8.674 1.00 0.64 ATOM 47 HG1 THR 22 10.954 5.507 -8.311 1.00 1.05 ATOM 48 CG2 THR 22 8.703 3.184 -8.484 1.00 0.62 ATOM 49 HG21 THR 22 9.401 2.413 -8.775 1.00 1.17 ATOM 50 HG22 THR 22 8.172 3.536 -9.357 1.00 1.27 ATOM 51 HG23 THR 22 7.997 2.781 -7.772 1.00 1.12 ATOM 52 C THR 22 7.341 5.150 -6.803 1.00 0.45 ATOM 53 O THR 22 6.295 4.765 -7.288 1.00 0.48 ATOM 54 N GLY 23 7.496 5.235 -5.511 1.00 0.42 ATOM 55 HN GLY 23 8.349 5.544 -5.140 1.00 0.42 ATOM 56 CA GLY 23 6.380 4.857 -4.596 1.00 0.43 ATOM 57 HA1 GLY 23 6.743 4.840 -3.580 1.00 0.46 ATOM 58 HA2 GLY 23 6.019 3.871 -4.855 1.00 0.47 ATOM 59 C GLY 23 5.238 5.867 -4.719 1.00 0.41 ATOM 60 O GLY 23 4.078 5.519 -4.618 1.00 0.47 ATOM 61 N ALA 24 5.551 7.114 -4.940 1.00 0.40 ATOM 62 HN ALA 24 6.492 7.377 -5.020 1.00 0.44 ATOM 63 CA ALA 24 4.476 8.137 -5.072 1.00 0.41 ATOM 64 HA ALA 24 3.756 8.008 -4.277 1.00 0.41 ATOM 65 CB ALA 24 5.086 9.537 -4.979 1.00 0.42 ATOM 66 HB1 ALA 24 5.621 9.635 -4.046 1.00 1.06 ATOM 67 HB2 ALA 24 4.299 10.276 -5.023 1.00 1.11 ATOM 68 HB3 ALA 24 5.768 9.688 -5.803 1.00 1.11 ATOM 69 C ALA 24 3.777 7.979 -6.425 1.00 0.41 ATOM 70 O ALA 24 2.601 8.254 -6.559 1.00 0.41 ATOM 71 N LEU 25 4.488 7.545 -7.434 1.00 0.42 ATOM 72 HN LEU 25 5.437 7.332 -7.312 1.00 0.43 ATOM 73 CA LEU 25 3.850 7.383 -8.774 1.00 0.44 ATOM 74 HA LEU 25 3.204 8.228 -8.955 1.00 0.43 ATOM 75 CB LEU 25 4.932 7.318 -9.858 1.00 0.47 ATOM 76 HB1 LEU 25 4.466 7.218 -10.826 1.00 0.85 ATOM 77 HB2 LEU 25 5.563 6.459 -9.676 1.00 0.82 ATOM 78 CG LEU 25 5.788 8.594 -9.825 1.00 0.77 ATOM 79 HG LEU 25 6.045 8.824 -8.801 1.00 1.46 ATOM 80 CD1 LEU 25 7.071 8.364 -10.628 1.00 1.58 ATOM 81 HD11 LEU 25 7.633 9.285 -10.680 1.00 2.16 ATOM 82 HD12 LEU 25 6.819 8.040 -11.627 1.00 2.10 ATOM 83 HD13 LEU 25 7.668 7.606 -10.144 1.00 2.08 ATOM 84 CD2 LEU 25 5.014 9.773 -10.436 1.00 1.67 ATOM 85 HD21 LEU 25 5.701 10.577 -10.660 1.00 2.29 ATOM 86 HD22 LEU 25 4.275 10.125 -9.733 1.00 2.15 ATOM 87 HD23 LEU 25 4.524 9.459 -11.346 1.00 2.16 ATOM 88 C LEU 25 3.025 6.093 -8.796 1.00 0.44 ATOM 89 O LEU 25 1.879 6.086 -9.201 1.00 0.46 ATOM 90 N LEU 26 3.597 5.002 -8.363 1.00 0.45 ATOM 91 HN LEU 26 4.522 5.029 -8.040 1.00 0.46 ATOM 92 CA LEU 26 2.845 3.712 -8.358 1.00 0.47 ATOM 93 HA LEU 26 2.686 3.389 -9.377 1.00 0.49 ATOM 94 CB LEU 26 3.665 2.650 -7.581 1.00 0.51 ATOM 95 HB1 LEU 26 3.043 2.172 -6.836 1.00 0.81 ATOM 96 HB2 LEU 26 4.492 3.137 -7.087 1.00 0.80 ATOM 97 CG LEU 26 4.215 1.575 -8.536 1.00 0.69 ATOM 98 HG LEU 26 3.403 1.165 -9.120 1.00 1.43 ATOM 99 CD1 LEU 26 5.257 2.190 -9.476 1.00 1.17 ATOM 100 HD11 LEU 26 4.758 2.779 -10.229 1.00 1.78 ATOM 101 HD12 LEU 26 5.822 1.402 -9.954 1.00 1.70 ATOM 102 HD13 LEU 26 5.927 2.820 -8.910 1.00 1.68 ATOM 103 CD2 LEU 26 4.867 0.459 -7.716 1.00 1.35 ATOM 104 HD21 LEU 26 4.152 0.065 -7.010 1.00 1.84 ATOM 105 HD22 LEU 26 5.719 0.855 -7.183 1.00 1.93 ATOM 106 HD23 LEU 26 5.193 -0.330 -8.378 1.00 1.89 ATOM 107 C LEU 26 1.479 3.932 -7.690 1.00 0.49 ATOM 108 O LEU 26 0.475 3.402 -8.123 1.00 0.52 ATOM 109 N LEU 27 1.436 4.708 -6.641 1.00 0.50 ATOM 110 HN LEU 27 2.256 5.126 -6.306 1.00 0.49 ATOM 111 CA LEU 27 0.137 4.956 -5.954 1.00 0.56 ATOM 112 HA LEU 27 -0.407 4.026 -5.884 1.00 0.58 ATOM 113 CB LEU 27 0.408 5.514 -4.550 1.00 0.64 ATOM 114 HB1 LEU 27 1.072 6.362 -4.626 1.00 1.04 ATOM 115 HB2 LEU 27 0.876 4.749 -3.948 1.00 1.45 ATOM 116 CG LEU 27 -0.900 5.955 -3.878 1.00 0.95 ATOM 117 HG LEU 27 -1.329 6.782 -4.425 1.00 1.71 ATOM 118 CD1 LEU 27 -1.897 4.789 -3.849 1.00 1.66 ATOM 119 HD11 LEU 27 -2.657 4.980 -3.105 1.00 2.02 ATOM 120 HD12 LEU 27 -1.378 3.874 -3.605 1.00 2.23 ATOM 121 HD13 LEU 27 -2.365 4.690 -4.818 1.00 2.21 ATOM 122 CD2 LEU 27 -0.594 6.403 -2.445 1.00 1.42 ATOM 123 HD21 LEU 27 0.043 7.274 -2.469 1.00 1.98 ATOM 124 HD22 LEU 27 -0.093 5.605 -1.918 1.00 1.93 ATOM 125 HD23 LEU 27 -1.517 6.645 -1.939 1.00 1.88 ATOM 126 C LEU 27 -0.680 5.958 -6.774 1.00 0.56 ATOM 127 O LEU 27 -1.894 5.938 -6.766 1.00 0.60 ATOM 128 N GLN 28 -0.025 6.834 -7.486 1.00 0.55 ATOM 129 HN GLN 28 0.955 6.835 -7.482 1.00 0.53 ATOM 130 CA GLN 28 -0.768 7.831 -8.305 1.00 0.58 ATOM 131 HA GLN 28 -1.574 8.248 -7.719 1.00 0.65 ATOM 132 CB GLN 28 0.183 8.952 -8.731 1.00 0.60 ATOM 133 HB1 GLN 28 0.903 8.564 -9.435 1.00 0.92 ATOM 134 HB2 GLN 28 0.698 9.336 -7.862 1.00 0.99 ATOM 135 CG GLN 28 -0.618 10.076 -9.390 1.00 1.00 ATOM 136 HG1 GLN 28 -1.345 10.459 -8.690 1.00 1.50 ATOM 137 HG2 GLN 28 -1.125 9.692 -10.263 1.00 1.47 ATOM 138 CD GLN 28 0.329 11.204 -9.804 1.00 1.40 ATOM 139 OE1 GLN 28 1.529 11.094 -9.646 1.00 2.09 ATOM 140 NE2 GLN 28 -0.163 12.291 -10.332 1.00 1.91 ATOM 141 HE21 GLN 28 -1.131 12.380 -10.459 1.00 2.26 ATOM 142 HE22 GLN 28 0.435 13.020 -10.601 1.00 2.37 ATOM 143 C GLN 28 -1.341 7.149 -9.550 1.00 0.54 ATOM 144 O GLN 28 -2.389 7.515 -10.043 1.00 0.58 ATOM 145 N GLY 29 -0.659 6.162 -10.064 1.00 0.50 ATOM 146 HN GLY 29 0.186 5.884 -9.653 1.00 0.50 ATOM 147 CA GLY 29 -1.162 5.460 -11.280 1.00 0.48 ATOM 148 HA1 GLY 29 -0.416 4.762 -11.626 1.00 0.50 ATOM 149 HA2 GLY 29 -1.363 6.186 -12.055 1.00 0.49 ATOM 150 C GLY 29 -2.447 4.701 -10.945 1.00 0.44 ATOM 151 O GLY 29 -3.488 4.938 -11.523 1.00 0.50 ATOM 152 N PHE 30 -2.382 3.785 -10.017 1.00 0.44 ATOM 153 HN PHE 30 -1.532 3.607 -9.563 1.00 0.53 ATOM 154 CA PHE 30 -3.600 3.009 -9.648 1.00 0.43 ATOM 155 HA PHE 30 -3.880 2.366 -10.470 1.00 0.42 ATOM 156 CB PHE 30 -3.307 2.159 -8.410 1.00 0.47 ATOM 157 HB1 PHE 30 -3.098 2.807 -7.571 1.00 0.54 ATOM 158 HB2 PHE 30 -2.449 1.531 -8.602 1.00 0.46 ATOM 159 CG PHE 30 -4.506 1.292 -8.096 1.00 0.47 ATOM 160 CD1 PHE 30 -4.862 0.254 -8.965 1.00 1.20 ATOM 161 HD1 PHE 30 -4.281 0.075 -9.858 1.00 2.10 ATOM 162 CD2 PHE 30 -5.261 1.522 -6.937 1.00 1.39 ATOM 163 HD2 PHE 30 -4.989 2.322 -6.264 1.00 2.27 ATOM 164 CE1 PHE 30 -5.970 -0.552 -8.678 1.00 1.21 ATOM 165 HE1 PHE 30 -6.244 -1.353 -9.349 1.00 2.09 ATOM 166 CE2 PHE 30 -6.369 0.715 -6.651 1.00 1.42 ATOM 167 HE2 PHE 30 -6.950 0.893 -5.759 1.00 2.33 ATOM 168 CZ PHE 30 -6.723 -0.322 -7.521 1.00 0.58 ATOM 169 HZ PHE 30 -7.577 -0.944 -7.300 1.00 0.65 ATOM 170 C PHE 30 -4.752 3.971 -9.348 1.00 0.40 ATOM 171 O PHE 30 -5.900 3.684 -9.623 1.00 0.43 ATOM 172 X ANI 500 97.272 4.212 -10.666 1.00 9.83 ATOM 173 Y ANI 500 96.938 1.142 -7.779 1.00 9.70 ATOM 174 Z ANI 500 94.761 0.905 -11.394 1.00 9.22 ATOM 175 OO ANI 500 94.992 2.933 -9.195 1.00 9.12 END coor copy end !!delete select (resid 502) end !---------------------------------------------------------------------- ! set the weights for the experimental energy terms evaluate ($knoe = 25.0) ! noes evaluate ($khb = 50.0) ! hbond evaluate ($asym = 0.2) ! slope of NOE potential evaluate ($kcdi = 10.0) ! torsion angles evaluate ($ksani=0.55) evaluate ($khbda=50.0) ! hbond_angle correlation evaluate ($cool_steps = 8000) evaluate ($init_t = 8000.00) !---------------------------------------------------------------------- ! The next statement makes sure the experimental energies are used in the ! calculation, and switches off the unwanted energy terms. ! note that the NMR torsions are only switched on in the cooling stage ! we include the noncrystallographic symmetry right from the start !--------------------------------------------------------------------------- ! Read experimental restraints noe nres = 16000 set echo on message on end class dist !@3dnoe_s.tbl assign ( resid 21 and name HN ) ( resid 22 and name HN ) 2.6 2.6 1.0 assign ( resid 22 and name HN ) ( resid 23 and name HN ) 2.7 2.7 1.0 assign ( resid 23 and name HN ) ( resid 24 and name HN ) 2.7 2.7 0.9 assign ( resid 24 and name HN ) ( resid 25 and name HN ) 2.5 2.5 0.8 assign ( resid 25 and name HN ) ( resid 26 and name HN ) 2.6 2.6 1.0 assign ( resid 26 and name HN ) ( resid 27 and name HN ) 2.6 2.6 0.9 assign ( resid 27 and name HN ) ( resid 28 and name HN ) 2.8 2.8 1.0 assign ( resid 29 and name HN ) ( resid 30 and name HN ) 2.8 2.8 1.0 !@cn4d_s.tbl assign ( resid 20 and name HA ) ( resid 21 and name HN ) 3.8 3.8 1.3 assign ( resid 20 and name HA ) ( resid 23 and name HN ) 4.2 1.5 1.5 assign ( resid 20 and name HA ) ( resid 24 and name HN ) 3.9 1.4 1.4 assign ( resid 20 and ( name HB1 or name HB2 )) ( resid 20 and name HN ) 3.6 3.6 1.3 assign ( resid 20 and ( name HB1 or name HB2 )) ( resid 21 and name HN ) 3.8 3.8 1.4 assign ( resid 20 and ( name HB2 or name HB1 )) ( resid 20 and name HN ) 3.7 3.7 1.3 assign ( resid 20 and ( name HB2 or name HB1 )) ( resid 21 and name HN ) 3.8 3.8 1.3 assign ( resid 20 and name HE# ) ( resid 20 and name HN ) 3.9 3.9 1.4 assign ( resid 20 and ( name HG1 or name HG2 )) ( resid 20 and name HN ) 3.7 3.7 1.3 assign ( resid 20 and ( name HG2 or name HG1 )) ( resid 20 and name HN ) 3.6 3.6 1.3 assign ( resid 20 and name HN ) ( resid 21 and name HB# ) 4.2 4.2 1.4 assign ( resid 21 and name HA ) ( resid 22 and name HN ) 3.6 3.6 1.3 assign ( resid 21 and name HA ) ( resid 24 and name HN ) 3.5 1.3 1.3 assign ( resid 21 and name HB# ) ( resid 21 and name HN ) 2.9 2.9 1.0 assign ( resid 21 and name HB# ) ( resid 22 and name HN ) 3.1 3.1 1.1 assign ( resid 21 and name HB# ) ( resid 23 and name HN ) 4.5 4.5 1.1 assign ( resid 21 and name HD# ) ( resid 21 and name HN ) 3.6 3.6 1.3 assign ( resid 21 and name HE# ) ( resid 21 and name HN ) 4.4 4.4 1.5 assign ( resid 21 and ( name HG1 or name HG2 )) ( resid 21 and name HN ) 3.4 3.4 1.1 assign ( resid 21 and ( name HG2 or name HG1 )) ( resid 21 and name HN ) 3.6 3.6 1.3 assign ( resid 21 and name HN ) ( resid 22 and name HA ) 4.5 4.5 1.5 assign ( resid 21 and name HN ) ( resid 22 and name HB ) 4.3 4.3 1.5 assign ( resid 22 and name HA ) ( resid 23 and name HN ) 4.1 4.1 1.4 assign ( resid 22 and name HA ) ( resid 24 and name HN ) 4.3 1.5 1.5 assign ( resid 22 and name HA ) ( resid 25 and name HN ) 3.5 1.3 1.3 assign ( resid 22 and name HA ) ( resid 26 and name HN ) 4.2 1.4 1.4 assign ( resid 22 and name HB ) ( resid 22 and name HN ) 3.1 3.1 1.1 assign ( resid 22 and name HB ) ( resid 23 and name HN ) 3.6 3.6 1.3 assign ( resid 22 and name HG2# ) ( resid 22 and name HN ) 3.4 3.4 1.1 assign ( resid 22 and name HG2# ) ( resid 26 and name HN ) 4.0 4.0 1.0 assign ( resid 22 and name HN ) ( resid 24 and name HB# ) 4.4 4.4 1.1 assign ( resid 23 and ( name HA1 or name HA2 )) ( resid 24 and name HN ) 3.5 3.5 1.3 assign ( resid 23 and ( name HA2 or name HA1 )) ( resid 24 and name HN ) 3.8 3.8 1.4 assign ( resid 24 and name HA ) ( resid 25 and name HN ) 3.9 3.9 1.4 assign ( resid 24 and name HA ) ( resid 27 and name HN ) 3.8 1.3 1.3 assign ( resid 24 and name HA ) ( resid 28 and name HN ) 4.6 1.5 1.5 assign ( resid 24 and name HB# ) ( resid 24 and name HN ) 2.8 2.8 1.0 assign ( resid 24 and name HB# ) ( resid 25 and name HN ) 3.0 3.0 1.0 assign ( resid 24 and name HB# ) ( resid 26 and name HN ) 4.3 4.3 1.1 assign ( resid 24 and name HN ) ( resid 25 and ( name HB1 or name HB2 )) 4.1 4.1 1.4 assign ( resid 25 and name HA ) ( resid 26 and name HN ) 4.1 4.1 1.4 assign ( resid 25 and name HA ) ( resid 28 and name HN ) 4.0 1.4 1.4 assign ( resid 25 and name HA ) ( resid 29 and name HN ) 4.2 1.5 1.5 assign ( resid 25 and ( name HB1 or name HB2 )) ( resid 25 and name HN ) 3.1 3.1 1.1 assign ( resid 25 and ( name HB1 or name HB2 )) ( resid 26 and name HN ) 3.5 3.5 1.3 assign ( resid 25 and ( name HB2 or name HB1 )) ( resid 25 and name HN ) 3.2 3.2 1.1 assign ( resid 25 and ( name HD1# or name HD2# )) ( resid 25 and name HN ) 3.3 3.3 1.1 assign ( resid 25 and ( name HD2# or name HD1# )) ( resid 25 and name HN ) 3.3 3.3 1.1 assign ( resid 25 and name HG ) ( resid 25 and name HN ) 3.0 3.0 1.1 assign ( resid 26 and name HA ) ( resid 27 and name HN ) 4.1 4.1 1.4 assign ( resid 26 and name HA ) ( resid 29 and name HN ) 4.5 1.5 1.5 assign ( resid 26 and ( name HB1 or name HB2 )) ( resid 27 and name HN ) 3.6 3.6 1.3 assign ( resid 26 and ( name HB2 or name HB1 )) ( resid 26 and name HN ) 3.5 3.5 1.3 assign ( resid 26 and ( name HD1# or name HD2# )) ( resid 26 and name HN ) 3.7 3.7 1.3 assign ( resid 26 and ( name HD2# or name HD1# )) ( resid 26 and name HN ) 3.4 3.4 1.1 assign ( resid 26 and name HG ) ( resid 26 and name HN ) 3.3 3.3 1.1 assign ( resid 27 and name HA ) ( resid 28 and name HN ) 4.5 4.5 1.5 assign ( resid 27 and name HA ) ( resid 30 and name HN ) 4.0 1.4 1.4 assign ( resid 27 and ( name HB1 or name HB2 )) ( resid 27 and name HN ) 3.3 3.3 1.1 assign ( resid 27 and ( name HB1 or name HB2 )) ( resid 28 and name HN ) 3.9 3.9 1.4 assign ( resid 27 and ( name HB2 or name HB1 )) ( resid 27 and name HN ) 3.2 3.2 1.1 assign ( resid 27 and ( name HB2 or name HB1 )) ( resid 28 and name HN ) 4.2 4.2 1.4 assign ( resid 27 and ( name HD1# or name HD2# )) ( resid 27 and name HN ) 3.7 3.7 1.3 assign ( resid 27 and name HG ) ( resid 27 and name HN ) 4.5 4.5 1.5 assign ( resid 28 and name HA ) ( resid 29 and name HN ) 4.2 4.2 1.4 assign ( resid 28 and ( name HB1 or name HB2 )) ( resid 28 and name HN ) 3.3 3.3 1.1 assign ( resid 28 and ( name HB1 or name HB2 )) ( resid 29 and name HN ) 3.5 3.5 1.3 assign ( resid 28 and ( name HB2 or name HB1 )) ( resid 28 and name HN ) 3.3 3.3 1.1 assign ( resid 28 and ( name HB2 or name HB1 )) ( resid 29 and name HN ) 3.5 3.5 1.3 assign ( resid 28 and name HG# ) ( resid 28 and name HN ) 3.3 3.3 1.1 assign ( resid 28 and name HG# ) ( resid 30 and name HN ) 4.6 4.6 1.2 assign ( resid 29 and ( name HA1 or name HA2 )) ( resid 30 and name HN ) 3.7 3.7 1.3 assign ( resid 29 and ( name HA2 or name HA1 )) ( resid 30 and name HN ) 3.9 3.9 1.4 assign ( resid 30 and name HB# ) ( resid 30 and name HN ) 3.3 3.3 1.1 assign ( resid 30 and name HD# ) ( resid 30 and name HN ) 4.5 4.5 1.5 !@hchc_s.tbl assign ( resid 20 and name HA ) ( resid 20 and name HE# ) 3.2 3.2 1.1 assign ( resid 20 and name HA ) ( resid 20 and name HG# ) 3.8 3.8 1.3 assign ( resid 20 and name HA ) ( resid 20 and ( name HG1 or name HG2 )) 4.0 4.0 1.4 assign ( resid 20 and name HA ) ( resid 20 and ( name HG2 or name HG1 )) 4.2 4.2 1.5 !(inter)assign ( resid 20 and name HA ) ( resid 21 and name HA ) 4.7 1.6 1.6 assign ( resid 20 and name HA ) ( resid 23 and ( name HA1 or name HA2 )) 4.7 4.7 1.2 assign ( resid 20 and ( name HB1 or name HB2 )) ( resid 20 and name HE# ) 3.9 3.9 1.4 !(inter)assign ( resid 20 and ( name HB1 or name HB2 )) ( resid 21 and name HE# ) 3.3 3.3 1.1 assign ( resid 20 and name HE# ) ( resid 20 and name HG# ) 3.1 3.1 1.1 assign ( resid 20 and name HE# ) ( resid 20 and ( name HG1 or name HG2 )) 3.5 3.5 1.2 assign ( resid 20 and name HE# ) ( resid 20 and ( name HG2 or name HG1 )) 3.6 3.6 1.3 assign ( resid 20 and name HE# ) ( resid 24 and name HB# ) 3.8 3.8 1.0 assign ( resid 21 and name HA ) ( resid 21 and name HE# ) 3.4 3.4 1.2 assign ( resid 21 and name HA ) ( resid 21 and ( name HG1 or name HG2 )) 3.3 3.3 1.2 assign ( resid 21 and name HA ) ( resid 24 and name HB# ) 3.1 3.1 0.8 assign ( resid 21 and name HB# ) ( resid 25 and ( name HD1# or name HD2# )) 3.5 3.5 0.9 !(inter)assign ( resid 22 and name HA ) ( resid 22 and name HG2# ) 3.1 3.1 1.1 assign ( resid 22 and name HA ) ( resid 25 and ( name HB1 or name HB2 )) 3.5 3.5 0.9 assign ( resid 22 and name HA ) ( resid 25 and ( name HB2 or name HB1 )) 3.7 3.7 0.9 assign ( resid 22 and name HA ) ( resid 25 and ( name HD1# or name HD2# )) 3.2 3.2 0.8 assign ( resid 22 and name HA ) ( resid 25 and name HG ) 3.9 1.4 1.4 !(inter)assign ( resid 22 and name HG2#) ( resid 23 and ( name HA2 or name HA1 )) 4.4 4.4 1.5 assign ( resid 22 and name HG2#) ( resid 26 and ( name HB1 or name HB2 )) 4.0 4.0 1.0 assign ( resid 22 and name HG2#) ( resid 26 and ( name HD1# or name HD2# )) 3.1 3.1 0.8 assign ( resid 22 and name HG2# ) ( resid 26 and name HG ) 3.6 3.6 0.9 assign ( resid 24 and name HA ) ( resid 27 and ( name HB1 or name HB2 )) 4.3 4.3 1.1 assign ( resid 24 and name HA ) ( resid 27 and ( name HB2 or name HB1 )) 4.3 4.3 1.1 assign ( resid 24 and name HA ) ( resid 27 and ( name HD1# or name HD2# )) 4.1 4.1 1.0 assign ( resid 24 and name HB# ) ( resid 25 and name HA ) 3.9 3.9 1.4 !(inter)assign ( resid 24 and name HB# ) ( resid 25 and ( name HB1 or name HB2 )) 3.9 3.9 1.4 assign ( resid 25 and name HA ) ( resid 25 and ( name HD1# or name HD2# )) 3.1 3.1 1.1 assign ( resid 25 and name HA ) ( resid 25 and ( name HD2# or name HD1# )) 2.9 2.9 1.0 assign ( resid 25 and name HA ) ( resid 25 and name HG ) 3.5 3.5 1.2 assign ( resid 25 and name HA ) ( resid 28 and name HG# ) 4.0 4.0 1.0 assign ( resid 25 and ( name HB1 or name HB2 )) ( resid 25 and ( name HD2# or name HD1# )) 3.1 3.1 1.1 assign ( resid 25 and ( name HB2 or name HB1 )) ( resid 25 and ( name HD1# or name HD2# )) 3.1 3.1 1.1 assign ( resid 25 and ( name HD2# or name HD1# )) ( resid 28 and ( name HB2 or name HB1 )) 3.9 3.9 1.0 assign ( resid 26 and name HA ) ( resid 26 and ( name HD1# or name HD2# )) 3.8 3.8 1.3 assign ( resid 26 and name HA ) ( resid 26 and ( name HD2# or name HD1# )) 3.0 3.0 1.0 assign ( resid 26 and name HA ) ( resid 26 and name HG ) 3.9 3.9 1.4 assign ( resid 26 and ( name HB1 or name HB2 )) ( resid 26 and ( name HD1# or name HD2# )) 3.5 3.5 1.2 assign ( resid 26 and ( name HB1 or name HB2 )) ( resid 26 and ( name HD2# or name HD1# )) 3.5 3.5 1.2 assign ( resid 26 and ( name HB2 or name HB1 )) ( resid 26 and ( name HD1# or name HD2# )) 3.6 3.6 1.2 assign ( resid 26 and ( name HB2 or name HB1 )) ( resid 26 and ( name HD2# or name HD1# )) 3.6 3.6 1.3 assign ( resid 27 and name HA ) ( resid 27 and ( name HD1# or name HD2# )) 4.0 4.0 1.4 assign ( resid 27 and name HA ) ( resid 27 and ( name HD2# or name HD1# )) 3.1 3.1 1.1 assign ( resid 27 and name HA ) ( resid 27 and name HG ) 4.2 4.2 1.5 assign ( resid 27 and ( name HB1 or name HB2 )) ( resid 27 and ( name HD2# or name HD1# )) 3.8 3.8 1.3 assign ( resid 27 and ( name HB2 or name HB1 )) ( resid 27 and ( name HD1# or name HD2# )) 3.5 3.5 1.2 assign ( resid 27 and ( name HB2 or name HB1 )) ( resid 27 and ( name HD2# or name HD1# )) 3.6 3.6 1.3 assign ( resid 27 and ( name HD2# or name HD1# )) ( resid 30 and ( name HB2 or name HB1 )) 4.1 4.1 1.0 assign ( resid 28 and name HA ) ( resid 28 and name HG# ) 3.1 3.1 1.1 assign ( resid 30 and name HA ) ( resid 30 and name HD# ) 3.5 3.5 1.2 class hb !@hbond_s.tbl assign ( resid 20 and name O ) ( resid 24 and name HN ) 1.9 0.4 0.6 assign ( resid 20 and name O ) ( resid 24 and name N ) 2.9 0.5 0.7 assign ( resid 21 and name O ) ( resid 25 and name HN ) 1.9 0.4 0.6 assign ( resid 21 and name O ) ( resid 25 and name N ) 2.9 0.5 0.7 assign ( resid 22 and name O ) ( resid 26 and name HN ) 1.9 0.4 0.6 assign ( resid 22 and name O ) ( resid 26 and name N ) 2.9 0.5 0.7 assign ( resid 23 and name O ) ( resid 27 and name HN ) 1.9 0.4 0.6 assign ( resid 23 and name O ) ( resid 27 and name N ) 2.9 0.5 0.7 assign ( resid 24 and name O ) ( resid 28 and name HN ) 1.9 0.4 0.6 assign ( resid 24 and name O ) ( resid 28 and name N ) 2.9 0.5 0.7 assign ( resid 25 and name O ) ( resid 29 and name HN ) 1.9 0.4 0.6 assign ( resid 25 and name O ) ( resid 29 and name N ) 2.9 0.5 0.7 assign ( resid 26 and name O ) ( resid 30 and name HN ) 1.9 0.4 0.6 assign ( resid 26 and name O ) ( resid 30 and name N ) 2.9 0.5 0.7 end noe ceiling 100 averaging dist sum potential dist soft !soft scale dist $knoe sqconstant dist 1.0 sqexponent dist 2 soexponent dist 1 rswitch dist 0.6 sqoffset dist 0.0 asymptote dist 2.0 averaging hb sum potential hb square scale hb $khb sqconstant hb 1.0 sqexponent hb 2 end restraints dihed scale $kcdi nass = 400 !@phi_s.tbl assign ( resid 20 and name C ) ( resid 21 and name N ) ( resid 21 and name CA ) ( resid 21 and name C ) 5.00 -65.13 30.00 2 assign ( resid 21 and name C ) ( resid 22 and name N ) ( resid 22 and name CA ) ( resid 22 and name C ) 5.00 -64.15 30.00 2 assign ( resid 22 and name C ) ( resid 23 and name N ) ( resid 23 and name CA ) ( resid 23 and name C ) 5.00 -60.36 30.00 2 assign ( resid 23 and name C ) ( resid 24 and name N ) ( resid 24 and name CA ) ( resid 24 and name C ) 5.00 -63.25 30.00 2 assign ( resid 24 and name C ) ( resid 25 and name N ) ( resid 25 and name CA ) ( resid 25 and name C ) 5.00 -62.62 30.00 2 assign ( resid 25 and name C ) ( resid 26 and name N ) ( resid 26 and name CA ) ( resid 26 and name C ) 5.00 -63.73 30.00 2 assign ( resid 26 and name C ) ( resid 27 and name N ) ( resid 27 and name CA ) ( resid 27 and name C ) 5.00 -61.84 30.00 2 assign ( resid 27 and name C ) ( resid 28 and name N ) ( resid 28 and name CA ) ( resid 28 and name C ) 5.00 -62.05 30.00 2 assign ( resid 28 and name C ) ( resid 29 and name N ) ( resid 29 and name CA ) ( resid 29 and name C ) 5.00 -63.37 30.00 2 assign ( resid 29 and name C ) ( resid 30 and name N ) ( resid 30 and name CA ) ( resid 30 and name C ) 5.00 -65.24 30.00 2 !@psi_s.tbl assign ( resid 20 and name N ) ( resid 20 and name CA ) ( resid 20 and name C ) ( resid 21 and name N ) 5.00 -36.38 30.00 2 assign ( resid 21 and name N ) ( resid 21 and name CA ) ( resid 21 and name C ) ( resid 22 and name N ) 5.00 -39.46 30.00 2 assign ( resid 22 and name N ) ( resid 22 and name CA ) ( resid 22 and name C ) ( resid 23 and name N ) 5.00 -43.45 30.00 2 assign ( resid 23 and name N ) ( resid 23 and name CA ) ( resid 23 and name C ) ( resid 24 and name N ) 5.00 -39.86 30.00 2 assign ( resid 24 and name N ) ( resid 24 and name CA ) ( resid 24 and name C ) ( resid 25 and name N ) 5.00 -41.68 30.00 2 assign ( resid 25 and name N ) ( resid 25 and name CA ) ( resid 25 and name C ) ( resid 26 and name N ) 5.00 -38.94 30.00 2 assign ( resid 26 and name N ) ( resid 26 and name CA ) ( resid 26 and name C ) ( resid 27 and name N ) 5.00 -40.14 30.00 2 assign ( resid 27 and name N ) ( resid 27 and name CA ) ( resid 27 and name C ) ( resid 28 and name N ) 5.00 -40.45 30.00 2 assign ( resid 28 and name N ) ( resid 28 and name CA ) ( resid 28 and name C ) ( resid 29 and name N ) 5.00 -42.31 30.00 2 assign ( resid 29 and name N ) ( resid 29 and name CA ) ( resid 29 and name C ) ( resid 30 and name N ) 5.00 -38.91 30.00 2 end evaluate ($kdnh = $ksani) evaluate ($kdch = 1.0*$kdnh) evaluate ($kdch3 = 0.5*$kdnh) evaluate ($kdcc = 2.0*$kdnh) set echo on message on end evaluate ($da=12.0) evaluate ($rhom=0.5) evaluate ($dac=$da*2.18) evaluate ($dacc=$da*0.2) set echo on message on end dipo nres=1000 class dnh type fixd scale 1.0 sign on average sum force $kdnh potential harmonic coef 0.0000 $da $rhom !@DNH_s.tbl assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 20 and name N ) ( resid 20 and name HN ) -7.7310 1.0000 1.0000 assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 21 and name N ) ( resid 21 and name HN ) -13.5980 1.0000 1.0000 assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 22 and name N ) ( resid 22 and name HN ) -19.1190 1.0000 1.0000 assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 23 and name N ) ( resid 23 and name HN ) -7.6530 1.0000 1.0000 assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 24 and name N ) ( resid 24 and name HN ) -5.5790 1.0000 1.0000 assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 25 and name N ) ( resid 25 and name HN ) -20.4920 1.0000 1.0000 assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 26 and name N ) ( resid 26 and name HN ) -14.9360 1.0000 1.0000 assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 27 and name N ) ( resid 27 and name HN ) -5.6340 1.0000 1.0000 assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 28 and name N ) ( resid 28 and name HN ) -8.1150 1.0000 1.0000 assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 29 and name N ) ( resid 29 and name HN ) -18.3580 1.0000 1.0000 ! class dch ! type fixd ! scale 1.0 ! sign on ! average sum ! force $kdch ! potential harmonic ! coef 0.0000 $dac $rhom ! @DCH_s.tbl ! class dch3 ! type fixd ! scale 1.0 ! sign on ! average sum ! force $kdch3 ! potential square ! coef 0.0000 $dac $rhom ! @DCH3.tbl end set echo on message on end evaluate ($kcsa = 0.0001) evaluate ($dacs = 12.0) evaluate ($rhcs = 0.5) dcsa nres=200 class heli scale 21652.1 force $kcsa type carb potential harmonic coeff 0.0 $dacs $rhcs ! sigma 74.7 11.8 -86.5 sigma 71.2 23.3 -94.5 !@baxcsa_s.tbl assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 20 and name C ) ( resid 20 and name O ) ( resid 21 and name N ) -31.25 5.00 5.00 assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 21 and name C ) ( resid 21 and name O ) ( resid 22 and name N ) 65.64 5.00 5.00 assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 22 and name C ) ( resid 22 and name O ) ( resid 23 and name N ) -32.09 5.00 5.00 assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 23 and name C ) ( resid 23 and name O ) ( resid 24 and name N ) 3.10 5.00 5.00 assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 24 and name C ) ( resid 24 and name O ) ( resid 25 and name N ) 35.90 5.00 5.00 assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 25 and name C ) ( resid 25 and name O ) ( resid 26 and name N ) -31.21 5.00 5.00 assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 26 and name C ) ( resid 26 and name O ) ( resid 27 and name N ) 38.45 5.00 5.00 assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 27 and name C ) ( resid 27 and name O ) ( resid 28 and name N ) -63.20 5.00 5.00 assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 28 and name C ) ( resid 28 and name O ) ( resid 29 and name N ) 77.41 5.00 5.00 assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 29 and name C ) ( resid 29 and name O ) ( resid 30 and name N ) -64.73 5.00 5.00 end hbda nres=300 class hbon force $khbda !@hbda_s.tbl assign ( resid 24 and name N ) ( resid 24 and name HN) ( resid 20 and name O ) assign ( resid 25 and name N ) ( resid 25 and name HN) ( resid 21 and name O ) assign ( resid 26 and name N ) ( resid 26 and name HN) ( resid 22 and name O ) assign ( resid 27 and name N ) ( resid 27 and name HN) ( resid 23 and name O ) assign ( resid 28 and name N ) ( resid 28 and name HN) ( resid 24 and name O ) assign ( resid 29 and name N ) ( resid 29 and name HN) ( resid 25 and name O ) assign ( resid 30 and name N ) ( resid 30 and name HN) ( resid 26 and name O ) end !!evaluate ($rcon = 0.004) !!parameters !! nbonds !! atom !! nbxmod 3 !! wmin = 0.01 ! warning off !! cutnb = 4.5 ! nonbonded cutoff !! tolerance 0.5 !! repel= 0.9 ! scale factor for vdW radii = 1 ( L-J radii) !! rexp = 2 ! exponents in (r^irex - R0^irex)^rexp !! irex = 2 !! rcon=$rcon ! actually set the vdW weight !! end !!end set message on echo on end ! Fixing the axis using harmonic restraint ! leave out, let both rotate vector do (refx=x) (all) vector do (refy=y) (all) vector do (refz=z) (all) vector do (harmonic=20.0) (resid 500 and name OO) vector do (harmonic=0.0) (resid 500 and name Z ) vector do (harmonic=0.0) (resid 500 and name X ) vector do (harmonic=0.0) (resid 500 and name Y ) vector do (harmonic=0.0) (not (resid 500)) restraints harmonic exponent=2 end flags include harm end !!constraints fix (resid 500:501 and name OO) end !------------------------------------------------------------------- ! Set the Flags flags exclude * include bond angle impr vdw noe cdih harm dipo hbda !dcsa end !------------------------------------------------------------------ ! Dynamics: CA-CA vector do (mass = 100.0) (all) ! uniform mass for all atoms vector do (fbeta = 10.0) (all) ! coupling to heat bath evaluate ($count =0) while ($count < 1 ) loop structure evaluate ($count = $count + 1) coor swap end coor copy end evaluate ($ini_rad = 0.9) evaluate ($fin_rad = 0.80) evaluate ($ini_con= 0.004) evaluate ($fin_con= 4.0) evaluate ($ini_ncs = 0.01) evaluate ($fin_ncs = 10) evaluate ($ini_ang = 0.4) evaluate ($fin_ang = 1.0) evaluate ($ini_imp = 0.1) evaluate ($fin_imp = 1.0) evaluate ($ini_noe = 2.0) evaluate ($fin_noe = 50.0) evaluate ($ini_hb = 2.0) evaluate ($fin_hb = 50.0) evaluate ($knoe = $ini_noe) ! slope of NOE potential evaluate ($khb = 0.0001) ! slope of NOE potential evaluate ($kcdi = 10.0) ! torsion angles evaluate ($rcon = 0.004) ! force constant for vdW noe scale dist $knoe scale hb $khb end evaluate ($ini_sani = 0.001) evaluate ($fin_sani = 1.00) evaluate ($ksani = $ini_sani) ! slope of NOE potential evaluate ($ksani = 0.0001) ! dipolar coupling force constant evaluate ($kdnh = $ksani) evaluate ($kdch = 1.0*$kdnh) evaluate ($kdch3 = 0.5*$kdnh) evaluate ($kdcc = 2.0*$kdnh) dipo class dnh force $kdnh class dnh2 force $kdnh ! class dch force $kdch ! class dch2 force $kdch ! class dch3 force $kdch3 class dcc force $kdcc class dcc2 force $kdcc end evaluate ($ini_csa = 0.0001) evaluate ($fin_csa = .0009) evaluate ($kcsa = $ini_csa) dcsa class heli force $kcsa end evaluate ($ini_hbda = 2.0) evaluate ($fin_hbda = 500.0) evaluate ($khbda = $ini_hbda) hbda class hbon force $khbda end parameters nbonds atom nbxmod 3 wmin = 0.01 ! warning off cutnb = 100 ! nonbonded cutoff tolerance 45 repel= 1.2 ! scale factor for vdW radii = 1 ( L-J radii) rexp = 2 ! exponents in (r^irex - R0^irex)^rexp irex = 2 rcon=$rcon ! actually set the vdW weight end end constraints interaction (not name ca) (all) weights * 1 angl 0.4 impr 0.1 vdw 0 elec 0 end interaction (name ca) (name ca) weights * 1 angl 0.4 impr 0.1 vdw 1.0 end end !dynamics verlet ! nstep=1000 ! ! ! timestep=0.001 ! ! ! iasvel=maxwell firsttemp= $init_t ! tcoupling = true ! tbath = $init_t ! ! nprint=25 ! iprfrq=0 ! ntrfr = 99999999 !end !------------------------------------------------------------------- !Dynamics: All-All Loop parameters nbonds atom nbxmod 3 wmin = 0.01 ! warning off cutnb = 4.5 ! nonbonded cutoff tolerance 0.5 !! repel= 0.9 ! scale factor for vdW radii = 1 ( L-J radii) rexp = 2 ! exponents in (r^irex - R0^irex)^rexp irex = 2 !! rcon =1.0 ! actually set the vdW weight end end evaluate ($kcdi = 20) restraints dihed scale $kcdi end evaluate ($final_t = 100) { K } evaluate ($tempstep = 25) { K } evaluate ($ncycle = ($init_t-$final_t)/$tempstep) evaluate ($nstep = int($cool_steps*4.0/$ncycle)) evaluate ($bath = $init_t) evaluate ($k_vdw = $ini_con) evaluate ($k_vdwfact = ($fin_con/$ini_con)^(1/$ncycle)) evaluate ($radius= $ini_rad) evaluate ($radfact = ($fin_rad/$ini_rad)^(1/$ncycle)) evaluate ($k_ang = $ini_ang) evaluate ($ang_fac = ($fin_ang/$ini_ang)^(1/$ncycle)) evaluate ($k_imp = $ini_imp) evaluate ($imp_fac = ($fin_imp/$ini_imp)^(1/$ncycle)) evaluate ($noe_fac = ($fin_noe/$ini_noe)^(1/$ncycle)) evaluate ($knoe = $ini_noe) !!evaluate ($khb = $ini_hb) !!evaluate ($hb_fac = ($fin_hb/$ini_hb)^(1/$cycle)) evaluate ($sani_fac = ($fin_sani/$ini_sani)^(1/$ncycle)) evaluate ($ksani = $ini_sani) evaluate ($kdnh = $ksani) evaluate ($kdch = 1.0*$kdnh) evaluate ($kdch3 = 0.5*$kdnh) evaluate ($kdcc = 2.0*$kdnh) evaluate ($csa_fac = ($fin_csa/$ini_csa)^(1/$ncycle)) evaluate ($kcsa = $ini_csa) vector do (vx = maxwell($bath)) (all) vector do (vy = maxwell($bath)) (all) vector do (vz = maxwell($bath)) (all) !evaluate ($i_cool = 0) !while ($i_cool < $ncycle) loop cool ! evaluate ($i_cool=$i_cool+1) ! ! evaluate ($bath = $bath - $tempstep) ! evaluate ($k_vdw=min($fin_con,$k_vdw*$k_vdwfact)) ! evaluate ($radius=max($fin_rad,$radius*$radfact)) ! evaluate ($k_ang = $k_ang*$ang_fac) ! evaluate ($k_imp = $k_imp*$imp_fac) ! evaluate ($knoe = $knoe*$noe_fac) !!! evaluate ($khb=$khb*$hb_fac) ! !evaluate ($ksani = $ksani*$sani_fac) !evaluate ($kdnh = $ksani) !evaluate ($kdch = 1.0*$kdnh) !evaluate ($kdch3 = 0.5*$kdnh) !evaluate ($kdcc = 2.0*$kdnh) !evaluate ($kcsa = $kcsa*$csa_fac) ! ! ! !parameter reset @parallhdg_new_db.pro @zn.pro end ! constraints interaction (all) (all) weights ! * 1 angles $k_ang improper $k_imp ! end end ! parameter ! nbonds ! cutnb=4.5 rcon=$k_vdw nbxmod=3 repel=$radius ! end end ! ! noe scale dist $knoe ! scale hb $khb !end ! !dipo ! class dnh force $kdnh ! class dnh2 force $kdnh !! class dch force $kdch !! class dch2 force $kdch !! class dch3 force $kdch3 ! class dcc force $kdcc ! class dcc2 force $kdcc !end ! !dcsa ! class heli force $kcsa !end ! !hbda ! class hbon force $khbda !end ! ! dynamics verlet ! nstep=$nstep timestep=0.002 iasvel=current firsttemp= $bath ! tcoupling = true tbath = $bath nprint=$nstep iprfrq=0 ! ntrfr = 99999999 ! end !end loop cool !---------------------------------------------------------------- !Minimize: All-All mini powell nstep= 50 nprint= 50 end !-------------------------------------------------------------------- !Minimize CA-CA evaluate ($knoe = 2.0) ! slope of NOE potential evaluate ($khb = 2.0) ! slope of NOE potential evaluate ($ksani = 0.0001) ! dipolar force constant evaluate ($kcdi = 10.0) !torsion angles evaluate ($kcsa = 0.001) noe scale dist $knoe scale hb $khb end evaluate ($kdnh = $ksani) evaluate ($kdch = 1.0*$kdnh) evaluate ($kdch3 = 0.5*$kdnh) evaluate ($kdcc = 2.0*$kdnh) dipo class dnh force $kdnh class dnh2 force $kdnh ! class dch force $kdch ! class dch2 force $kdch ! class dch3 force $kdch3 class dcc force $kdcc class dcc2 force $kdcc end dcsa class heli force $kcsa end hbda class hbon force $khbda end restraints dihed scale $kcdi end evaluate ($rcon = 1.0) parameters nbonds atom nbxmod 3 wmin = 0.01 ! warning off cutnb = 100 ! nonbonded cutoff tolerance 45 repel= 1.2 ! scale factor for vdW radii = 1 ( L-J radii) rexp = 2 ! exponents in (r^irex - R0^irex)^rexp irex = 2 rcon=$rcon ! actually set the vdW weight end end constraints interaction (not name ca) (all) weights * 1 angl 0.4 impr 0.1 vdw 0 elec 0 end interaction (name ca) (name ca) weights * 1 angl 0.4 impr 0.1 vdw 1.0 end end !mini powell nstep = 250 nprint = 50 end !-------------------------------------------------------------------- !Minimize all-all loop parameters nbonds nbxmod 3 wmin = 0.01 ! warning off cutnb = 4.5 ! nonbonded cutoff tolerance 0.5 ! repel= 0.9-0.8 ! scale factor for vdW radii = 1 ( L-J radii) rexp = 2 ! exponents in (r^irex - R0^irex)^rexp irex = 2 ! rcon= 0.004-4 ! actually set the vdW weight end end evaluate ($kcdi = 20) restraints dihed scale $kcdi end evaluate ($final_t = 100) {K} evaluate ($tempstep = 50) {K} evaluate ($bath = $init_t) evaluate ($ncycle = ($init_t-$final_t)/$tempstep) evaluate ($nstep = int($cool_steps*4.0/$ncycle)) evaluate ($k_vdw = $ini_con) evaluate ($k_vdwfact = ($fin_con/$ini_con)^(1/$ncycle)) evaluate ($radius= $ini_rad) evaluate ($radfact = ($fin_rad/$ini_rad)^(1/$ncycle)) evaluate ($k_ncs = $ini_ncs) evaluate ($ncs_fac = ($fin_ncs/$ini_ncs)^(1/$ncycle)) evaluate ($k_ang = $ini_ang) evaluate ($ang_fac = ($fin_ang/$ini_ang)^(1/$ncycle)) evaluate ($k_imp = $ini_imp) evaluate ($imp_fac = ($fin_imp/$ini_imp)^(1/$ncycle)) evaluate ($knoe = $ini_noe) evaluate ($noe_fac = ($fin_noe/$ini_noe)^(1/$ncycle)) !!evaluate ($khb = $ini_hb) !!evaluate ($hb_fac = ($fin_hb/$ini_hb)^(1/$ncycle)) evaluate ($ksani = $ini_sani) evaluate ($kcsa = $ini_csa) evaluate ($csa_fac = ($fin_csa/$ini_csa)^(1/$ncycle)) evaluate ($khbda = $ini_hbda) evaluate ($hbda_fac = ($fin_hbda/$ini_hbda)^(1/$ncycle)) evaluate ($i_cool = 0) ! while ($i_cool < $ncycle) loop minim ! evaluate ($i_cool=$i_cool+1) ! ! evaluate ($bath = $bath - $tempstep) ! evaluate ($k_vdw=min($fin_con,$k_vdw*$k_vdwfact)) ! evaluate ($radius=max($fin_rad,$radius*$radfact)) ! evaluate ($k_ncs = $k_ncs*$ncs_fac) ! evaluate ($k_ang = $k_ang*$ang_fac) ! evaluate ($k_imp = $k_imp*$imp_fac) ! evaluate ($knoe = $knoe*$noe_fac) ! !! evaluate ($khb = $khb*$hb_fac) ! evaluate ($ksani = $ksani*$sani_fac) ! evaluate ($kcsa = $kcsa*$csa_fac) ! evaluate ($khbda = $khbda*$hbda_fac) ! ! evaluate ($kdnh = $ksani) ! evaluate ($kdch = 1.0*$kdnh) ! evaluate ($kdch3 = 0.5*$kdnh) ! evaluate ($kdcc = 2.0*$kdnh) ! ! constraints interaction (all) (all) weights ! * 1 angles $k_ang improper $k_imp ! end end ! ! parameter nbonds rcon=$k_vdw ! repel=$radius ! end end ! ! noe ! scale dist $knoe ! scale hb $khb ! end ! ! dipo ! class dnh force $kdnh ! class dnh2 force $kdnh ! ! class dch force $kdch ! ! class dch2 force $kdch ! ! class dch3 force $kdch3 ! class dcc force $kdcc ! class dcc2 force $kdcc ! end ! ! dcsa ! class heli force $kcsa ! end ! ! hbda ! class hbon force $khbda ! end ! ! mini powell nstep = 100 nprint = 50 end ! end loop minim !----------------------------------------------------- print threshold=0.3 noe evaluate ($rms_noe=$result) evaluate ($violations_noe=$violations) evaluate ($rms_hb=$result) evaluate ($violations_hb=$violations) print threshold=5. cdih evaluate ($rms_cdih=$result) evaluate ($violations_cdih=$violations) print thres=0.05 bonds evaluate ($rms_bonds=$result) print thres=5. angles evaluate ($rms_angles=$result) print thres=5. impropers evaluate ($rms_impropers=$result) couplings print threshold 0.5 class phi end evaluate ($rms_coup = $result) evaluate ($end_viols = $violations) dipo print threshold=1.0 class dnh end evaluate ($rms_DNH=$result) evaluate ($viol_DNH=$violations) dipo print threshold=1.0 class dnh2 end evaluate ($rms_DNH2=$result) evaluate ($viol_DNH2=$violations) dipo print threshold=1.0 class dch end evaluate ($rms_DCH=$result) evaluate ($viol_DCH=$violations) dipo print threshold=1.0 class dch2 end evaluate ($rms_DCH2=$result) evaluate ($viol_DCH2=$violations) dipo print threshold=1.0 class dch3 end evaluate ($rms_DCH3=$result) evaluate ($viol_DCH3=$violations) dipo print threshold=1.0 class dcc end evaluate ($rms_DCC=$result) evaluate ($viol_DCC=$violations) dipo print threshold=1.0 class dcc2 end evaluate ($rms_DCC2=$result) evaluate ($viol_DCC2=$violations) dcsa print threshold=1.0 class heli end evaluate ($rms_heli=$result) evaluate ($viol_heli=$violations) hbda print threshhold=0.0 class hbon end evaluate ($rms_hbon=$result) evaluate ($viol_hbon=$violations) remarks =============================================================== remarks overall,bonds,angles,improper,vdw,noe,cdih,coup,dipo,dcsa remarks energies: $ener,$bond,$angl,$impr,$vdw,$noe,$cdih,$coup,$dipo,$dcsa, remarks $hbda remarks =============================================================== remarks bonds,angles,impropers,noe remarks bonds etc: $rms_bonds,$rms_angles,$rms_impropers,$rms_noe remarks =============================================================== remarks noe remarks violations : $violations_noe remarks =============================================================== remarks dipo dnh dnh2 dch dch2 dch3 dcc dcc2 remarks RMS dipo: $rms_DNH $rms_DNH2 $rms_DCH $rms_DCH2 remarks $rms_DCH3 $rms_DCC $rms_DCC2 remarks dcsa csa remarks RMS dcsa :$rms_heli remarks hbda hbon remarks RMS hbda :$rms_hbon remarks =============================================================== {====>} {*Name(s) of the family of final structures.*} evaluate ($file = "short_" + encode($count) + ".pdb") write coor output= $file end end loop structure stop