/dports/science/plumed/plumed2-2.7.2/user-doc/tutorials/old_tutorials/belfast-9a/system/ |
H A D | conf.gro | 60 4LYS N 58 -0.106 -0.678 0.131 61 4LYS H 59 -0.008 -0.698 0.133 62 4LYS CA 60 -0.162 -0.592 0.234 63 4LYS HA 61 -0.260 -0.584 0.216 64 4LYS CB 62 -0.138 -0.657 0.371 65 4LYS HB1 63 -0.040 -0.671 0.384 66 4LYS HB2 64 -0.185 -0.745 0.374 67 4LYS CG 65 -0.190 -0.569 0.485 68 4LYS HG1 66 -0.286 -0.546 0.469 69 4LYS HG2 67 -0.136 -0.486 0.491 [all …]
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H A D | out.gro | 60 4LYS N 58 4.684 4.161 2.381 61 4LYS H 59 4.782 4.141 2.383 62 4LYS CA 60 4.628 4.247 2.484 63 4LYS HA 61 4.530 4.255 2.466 64 4LYS CB 62 4.652 4.182 2.621 65 4LYS HB1 63 4.750 4.168 2.634 66 4LYS HB2 64 4.605 4.094 2.624 67 4LYS CG 65 4.600 4.270 2.735 68 4LYS HG1 66 4.504 4.293 2.719 69 4LYS HG2 67 4.654 4.353 2.741 [all …]
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H A D | em.gro | 60 4LYS N 58 4.689 4.153 2.380 61 4LYS H 59 4.787 4.126 2.383 62 4LYS CA 60 4.642 4.250 2.480 63 4LYS HA 61 4.534 4.261 2.473 64 4LYS CB 62 4.674 4.195 2.621 65 4LYS HB1 63 4.780 4.173 2.628 66 4LYS HB2 64 4.619 4.101 2.635 67 4LYS CG 65 4.636 4.292 2.734 68 4LYS HG1 66 4.531 4.320 2.725 69 4LYS HG2 67 4.696 4.383 2.725 [all …]
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H A D | topol.top | 93 ; residue 4 LYS rtp LYS q +1.0 98 62 CT 4 LYS CB 62 -0.0094 12.01 ; qtot 0.82 115 79 O 4 LYS O 79 -0.5894 16 ; qtot 2 196 ; residue 10 LYS rtp LYS q +1.0 218 176 O 10 LYS O 176 -0.5894 16 ; qtot 3 254 ; residue 13 LYS rtp LYS q +1.0 276 231 O 13 LYS O 231 -0.5894 16 ; qtot 4 346 ; residue 19 LYS rtp LYS q +1.0 479 ; residue 28 LYS rtp LYS q +1.0 534 ; residue 31 LYS rtp LYS q +1.0 [all …]
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/tests/complete-test/ |
H A D | test-output-1AFS-ph-low-ph-correct.propka | 1071 LYS 28 A 10.49 10.50 1072 LYS 31 A 10.91 10.50 1073 LYS 36 A 11.46 10.50 1074 LYS 39 A 9.79 10.50 1075 LYS 68 A 11.53 10.50 1076 LYS 75 A 11.30 10.50 1077 LYS 84 A 8.66 10.50 1078 LYS 101 A 10.48 10.50 1079 LYS 104 A 10.43 10.50 1080 LYS 136 A 10.69 10.50 [all …]
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H A D | test-output-1AFS-ph-neutral-correct.propka | 1071 LYS 28 A 10.49 10.50 1072 LYS 31 A 10.91 10.50 1073 LYS 36 A 11.46 10.50 1074 LYS 39 A 9.79 10.50 1075 LYS 68 A 11.53 10.50 1076 LYS 75 A 11.30 10.50 1077 LYS 84 A 8.66 10.50 1078 LYS 101 A 10.48 10.50 1079 LYS 104 A 10.43 10.50 1080 LYS 136 A 10.69 10.50 [all …]
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/sg/examples/data/pqr/ |
H A D | fig001_asc.pqr | 36 ATOM 20 N LYS 2 3.510 10.167 -1.804 -0.470 1.550 37 ATOM 21 HN LYS 2 4.054 9.708 -1.106 0.310 1.200 38 ATOM 22 CA LYS 2 4.259 11.015 -2.694 0.070 1.700 39 ATOM 23 HA LYS 2 3.589 11.643 -3.264 0.090 1.200 40 ATOM 24 CB LYS 2 5.266 11.903 -1.928 -0.180 1.700 41 ATOM 25 HB1 LYS 2 5.845 12.529 -2.642 0.090 1.200 42 ATOM 26 HB2 LYS 2 5.983 11.259 -1.372 0.090 1.200 43 ATOM 27 CG LYS 2 4.567 12.832 -0.924 -0.180 1.700 44 ATOM 28 HG1 LYS 2 3.971 12.218 -0.214 0.090 1.200 45 ATOM 29 HG2 LYS 2 3.866 13.495 -1.477 0.090 1.200 [all …]
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/dports/science/py-MDAnalysisTests/MDAnalysisTests-0.19.2/MDAnalysisTests/data/ |
H A D | namd_cgenff.psf | 26 20 A002 10 LYS N NH1 -0.470000 14.0070 0 27 21 A002 10 LYS HN H 0.310000 1.0080 0 28 22 A002 10 LYS CA CT1 0.070000 12.0110 0 29 23 A002 10 LYS HA HB 0.090000 1.0080 0 30 24 A002 10 LYS CB CT2 -0.180000 12.0110 0 31 25 A002 10 LYS HB1 HA 0.090000 1.0080 0 32 26 A002 10 LYS HB2 HA 0.090000 1.0080 0 33 27 A002 10 LYS CG CT2 -0.180000 12.0110 0 34 28 A002 10 LYS HG1 HA 0.090000 1.0080 0 35 29 A002 10 LYS HG2 HA 0.090000 1.0080 0 [all …]
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H A D | adk_open.pqr | 187 ATOM 175 N LYS 13 -4.965 10.166 20.925 -0.4700 1.8500 188 ATOM 176 H LYS 13 -4.121 9.809 20.548 0.3100 0.2245 189 ATOM 177 CA LYS 13 -5.414 11.439 20.379 0.0700 2.2750 190 ATOM 178 HA LYS 13 -5.418 12.168 21.179 0.0900 1.3200 191 ATOM 179 CB LYS 13 -4.429 11.896 19.274 -0.1800 2.1750 192 ATOM 180 HB3 LYS 13 -3.516 12.294 19.760 0.0900 1.3200 193 ATOM 181 HB2 LYS 13 -4.878 12.743 18.708 0.0900 1.3200 194 ATOM 182 CG LYS 13 -3.992 10.783 18.308 -0.1800 2.1750 195 ATOM 183 HG3 LYS 13 -4.857 10.108 18.115 0.0900 1.3200 196 ATOM 184 HG2 LYS 13 -3.174 10.185 18.770 0.0900 1.3200 [all …]
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H A D | adk_open.crd | 179 175 13 LYS N -4.96500 10.16600 20.92500 4AKE 13 0.00000 180 176 13 LYS HN -4.12100 9.80900 20.54800 4AKE 13 0.00000 181 177 13 LYS CA -5.41400 11.43900 20.37900 4AKE 13 0.00000 182 178 13 LYS HA -5.41800 12.16800 21.17900 4AKE 13 0.00000 183 179 13 LYS CB -4.42900 11.89600 19.27400 4AKE 13 0.00000 184 180 13 LYS HB1 -3.51600 12.29400 19.76000 4AKE 13 0.00000 185 181 13 LYS HB2 -4.87800 12.74300 18.70800 4AKE 13 0.00000 186 182 13 LYS CG -3.99200 10.78300 18.30800 4AKE 13 0.00000 187 183 13 LYS HG1 -4.85700 10.10800 18.11500 4AKE 13 0.00000 188 184 13 LYS HG2 -3.17400 10.18500 18.77000 4AKE 13 0.00000 [all …]
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/dports/science/plumed/plumed2-2.7.2/user-doc/tutorials/lugano-6d/ |
H A D | GB1_start.gro | 30 4LYS N 28 7.936 5.414 7.713 -1.2086 -0.7318 1.1334 31 4LYS CA 29 7.880 5.413 7.845 0.4770 0.0713 1.8845 32 4LYS C 30 7.985 5.493 7.920 0.4307 1.5420 0.4444 33 4LYS O 31 8.086 5.542 7.867 0.7280 -0.7433 -1.2517 34 4LYS CB 32 7.890 5.263 7.881 0.7516 -0.3529 0.1295 35 4LYS CG 33 7.941 5.230 8.021 1.4955 -0.2498 -0.1104 36 4LYS CD 34 7.908 5.083 8.044 0.1879 -0.1553 -1.2480 37 4LYS CE 35 7.842 5.023 7.914 0.7972 1.1486 -2.1770 38 4LYS NZ 36 7.901 4.894 7.854 -0.2581 0.1619 -1.1353 75 10LYS N 73 6.725 5.673 7.714 -0.4484 1.1504 -1.3078 [all …]
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/contrib/iapbs/modules/Amber/test/pbsa_pgb/iAPBS/ |
H A D | pgb.pqr | 62 ATOM 55 N LYS 4 27.154 25.190 31.912 -0.4000 1.5000 63 ATOM 56 H LYS 4 26.195 25.072 32.208 0.4000 1.0000 64 ATOM 57 CA LYS 4 27.817 24.062 31.256 -0.0000 2.0000 65 ATOM 58 HA LYS 4 28.815 24.361 30.935 0.0000 0.0000 66 ATOM 59 CB LYS 4 27.976 22.939 32.292 0.0000 2.0000 67 ATOM 60 HB2 LYS 4 28.488 23.363 33.156 0.0000 0.0000 68 ATOM 61 HB3 LYS 4 26.995 22.590 32.616 0.0000 0.0000 69 ATOM 62 CG LYS 4 28.804 21.752 31.784 0.0000 2.0000 70 ATOM 63 HG2 LYS 4 28.233 21.192 31.043 0.0000 0.0000 71 ATOM 64 HG3 LYS 4 29.713 22.123 31.311 0.0000 0.0000 [all …]
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H A D | pgb-amber.pqr | 62 ATOM 55 N LYS 4 27.154 25.190 31.912 -0.3479 1.8240 63 ATOM 56 H LYS 4 26.195 25.072 32.208 0.2747 0.6000 64 ATOM 57 CA LYS 4 27.817 24.062 31.256 -0.2400 1.9080 65 ATOM 58 HA LYS 4 28.815 24.361 30.935 0.1426 1.3870 66 ATOM 59 CB LYS 4 27.976 22.939 32.292 -0.0094 1.9080 67 ATOM 60 HB2 LYS 4 28.488 23.363 33.156 0.0362 1.4870 68 ATOM 61 HB3 LYS 4 26.995 22.590 32.616 0.0362 1.4870 69 ATOM 62 CG LYS 4 28.804 21.752 31.784 0.0187 1.9080 70 ATOM 63 HG2 LYS 4 28.233 21.192 31.043 0.0103 1.4870 71 ATOM 64 HG3 LYS 4 29.713 22.123 31.311 0.0103 1.4870 [all …]
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H A D | pgb-parse.pqr | 62 ATOM 55 N LYS 4 27.154 25.190 31.912 -0.4000 1.5000 63 ATOM 56 H LYS 4 26.195 25.072 32.208 0.4000 1.0000 64 ATOM 57 CA LYS 4 27.817 24.062 31.256 -0.0000 2.0000 65 ATOM 58 HA LYS 4 28.815 24.361 30.935 0.0000 0.0000 66 ATOM 59 CB LYS 4 27.976 22.939 32.292 0.0000 2.0000 67 ATOM 60 HB2 LYS 4 28.488 23.363 33.156 0.0000 0.0000 68 ATOM 61 HB3 LYS 4 26.995 22.590 32.616 0.0000 0.0000 69 ATOM 62 CG LYS 4 28.804 21.752 31.784 0.0000 2.0000 70 ATOM 63 HG2 LYS 4 28.233 21.192 31.043 0.0000 0.0000 71 ATOM 64 HG3 LYS 4 29.713 22.123 31.311 0.0000 0.0000 [all …]
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/examples/bem/test_proteins/ |
H A D | 451c.pqr | 114 ATOM 118 N LYS 8 1.98200 -4.17300 15.37800 -0.47000 1.85000 115 ATOM 119 HN LYS 8 1.36072 -3.99513 14.61644 0.31000 0.22450 116 ATOM 120 CA LYS 8 2.00000 -3.14200 16.42000 0.07000 2.27500 117 ATOM 121 HA LYS 8 3.03160 -3.02112 16.72779 0.09000 1.32000 118 ATOM 122 CB LYS 8 1.36600 -1.86400 15.88400 -0.18000 2.17500 119 ATOM 123 HB1 LYS 8 0.74305 -2.15054 15.00527 0.09000 1.32000 120 ATOM 124 HB2 LYS 8 0.66318 -1.46068 16.64713 0.09000 1.32000 121 ATOM 125 CG LYS 8 2.37900 -0.81300 15.46300 -0.18000 2.17500 122 ATOM 126 HG1 LYS 8 1.84171 0.12697 15.20160 0.09000 1.32000 123 ATOM 127 HG2 LYS 8 3.04554 -0.58542 16.32648 0.09000 1.32000 [all …]
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/dports/biology/molden/molden5.8/test/ |
H A D | pdb.test | 69 REMARK 5 THR 99 TO LYS 71 REMARK 5 LYS 103 TO GLU 72 SEQRES 1 108 THR GLU PHE LYS ALA GLY SER ALA LYS LYS GLY ALA THR 73 SEQRES 2 108 LEU PHE LYS THR ARG CYS GLN GLN CYS HIS THR ILE GLU 74 SEQRES 3 108 GLU GLY GLY PRO ASN LYS VAL GLY PRO ASN LEU HIS GLY 75 SEQRES 4 108 ILE PHE GLY ARG HIS SER GLY GLN VAL LYS GLY TYR SER 76 SEQRES 5 108 TYR THR ASP ALA ASN ILE ASN LYS ASN VAL LYS TRP ASP 77 SEQRES 6 108 GLU ASP SER MET SER GLU TYR LEU THR ASN PRO LYS LYS 78 SEQRES 7 108 TYR ILE PRO GLY THR LYS MET ALA PHE GLY GLY LEU LYS 79 SEQRES 8 108 LYS GLU LYS ASP ARG ASN ASP LEU ILE THR TYR LEU LYS [all …]
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/trajectoryanalysis/tests/ |
H A D | lysozyme.gro | 3 1LYS N 1 3.536 2.234 -1.198 4 1LYS H1 2 3.612 2.288 -1.236 5 1LYS H2 3 3.470 2.214 -1.270 6 1LYS H3 4 3.492 2.286 -1.125 7 1LYS CA 5 3.589 2.107 -1.143 8 1LYS HA 6 3.633 2.055 -1.216 9 1LYS CB 7 3.687 2.144 -1.031 10 1LYS HB1 8 3.763 2.195 -1.070 11 1LYS HB2 9 3.639 2.201 -0.964 12 1LYS CG 10 3.745 2.025 -0.956 [all …]
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/pb_s_am/pbam/pbam_test_files/gtest/ |
H A D | test.pqr | 21 ATOM 20 N LYS 2 11.157 6.581 1.702 -0.3479 1.8240 22 ATOM 21 CA LYS 2 10.093 7.335 2.365 -0.2400 1.9080 23 ATOM 22 C LYS 2 8.730 6.742 2.022 0.7341 1.9080 24 ATOM 23 O LYS 2 7.724 7.102 2.633 -0.5894 1.6612 25 ATOM 24 CB LYS 2 10.143 8.807 1.909 -0.0094 1.9080 26 ATOM 25 CG LYS 2 11.477 9.442 2.336 0.0187 1.9080 27 ATOM 26 CD LYS 2 11.509 10.921 1.921 -0.0479 1.9080 28 ATOM 27 CE LYS 2 12.860 11.540 2.306 -0.0143 1.9080 29 ATOM 28 NZ LYS 2 13.085 11.369 3.769 -0.3854 1.8240 30 ATOM 29 H LYS 2 11.674 7.013 0.989 0.2747 0.6000 [all …]
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/pb_s_am/pbsam/pbsam_test_files/gtest/ |
H A D | test.pqr | 21 ATOM 20 N LYS 2 11.157 6.581 1.702 -0.3479 1.8240 22 ATOM 21 CA LYS 2 10.093 7.335 2.365 -0.2400 1.9080 23 ATOM 22 C LYS 2 8.730 6.742 2.022 0.7341 1.9080 24 ATOM 23 O LYS 2 7.724 7.102 2.633 -0.5894 1.6612 25 ATOM 24 CB LYS 2 10.143 8.807 1.909 -0.0094 1.9080 26 ATOM 25 CG LYS 2 11.477 9.442 2.336 0.0187 1.9080 27 ATOM 26 CD LYS 2 11.509 10.921 1.921 -0.0479 1.9080 28 ATOM 27 CE LYS 2 12.860 11.540 2.306 -0.0143 1.9080 29 ATOM 28 NZ LYS 2 13.085 11.369 3.769 -0.3854 1.8240 30 ATOM 29 H LYS 2 11.674 7.013 0.989 0.2747 0.6000 [all …]
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/examples/pka-lig/ |
H A D | bx6_7_bin_apbs.pqr | 40 ATOM 40 N LYS 16 37.683 -47.156 48.045 -0.400 1.830 41 ATOM 41 H LYS 16 37.823 -47.049 49.031 0.250 0.800 42 ATOM 42 CA LYS 16 38.434 -48.146 47.267 0.100 2.265 43 ATOM 43 CB LYS 16 39.704 -48.580 48.015 0.000 2.235 44 ATOM 44 CG LYS 16 39.446 -49.441 49.255 0.000 2.235 45 ATOM 45 CD LYS 16 40.691 -49.808 50.057 0.000 2.235 46 ATOM 46 CE LYS 16 40.325 -50.719 51.229 0.250 2.235 47 ATOM 47 NZ LYS 16 41.476 -50.882 52.125 -0.300 1.650 48 ATOM 48 HZ1 LYS 16 41.792 -49.942 52.438 0.350 0.600 49 ATOM 49 HZ2 LYS 16 42.250 -51.355 51.617 0.350 0.600 [all …]
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H A D | bx6_7_apo_apbs.pqr | 40 ATOM 40 N LYS 16 37.683 -47.156 48.045 -0.400 1.830 41 ATOM 41 H LYS 16 37.823 -47.049 49.031 0.250 0.800 42 ATOM 42 CA LYS 16 38.434 -48.146 47.267 0.100 2.265 43 ATOM 43 CB LYS 16 39.704 -48.580 48.015 0.000 2.235 44 ATOM 44 CG LYS 16 39.446 -49.441 49.255 0.000 2.235 45 ATOM 45 CD LYS 16 40.691 -49.808 50.057 0.000 2.235 46 ATOM 46 CE LYS 16 40.325 -50.719 51.229 0.250 2.235 47 ATOM 47 NZ LYS 16 41.476 -50.882 52.125 -0.300 1.650 48 ATOM 48 HZ1 LYS 16 41.792 -49.942 52.438 0.350 0.600 49 ATOM 49 HZ2 LYS 16 42.250 -51.355 51.617 0.350 0.600 [all …]
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/tools/matlab/solver/Examples/pka/ |
H A D | bx6_7_apo_apbs.pqr | 40 ATOM 40 N LYS 16 37.683 -47.156 48.045 -0.400 1.830 41 ATOM 41 H LYS 16 37.823 -47.049 49.031 0.250 0.800 42 ATOM 42 CA LYS 16 38.434 -48.146 47.267 0.100 2.265 43 ATOM 43 CB LYS 16 39.704 -48.580 48.015 0.000 2.235 44 ATOM 44 CG LYS 16 39.446 -49.441 49.255 0.000 2.235 45 ATOM 45 CD LYS 16 40.691 -49.808 50.057 0.000 2.235 46 ATOM 46 CE LYS 16 40.325 -50.719 51.229 0.250 2.235 47 ATOM 47 NZ LYS 16 41.476 -50.882 52.125 -0.300 1.650 48 ATOM 48 HZ1 LYS 16 41.792 -49.942 52.438 0.350 0.600 49 ATOM 49 HZ2 LYS 16 42.250 -51.355 51.617 0.350 0.600 [all …]
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H A D | bx6_7_bin_apbs.pqr | 40 ATOM 40 N LYS 16 37.683 -47.156 48.045 -0.400 1.830 41 ATOM 41 H LYS 16 37.823 -47.049 49.031 0.250 0.800 42 ATOM 42 CA LYS 16 38.434 -48.146 47.267 0.100 2.265 43 ATOM 43 CB LYS 16 39.704 -48.580 48.015 0.000 2.235 44 ATOM 44 CG LYS 16 39.446 -49.441 49.255 0.000 2.235 45 ATOM 45 CD LYS 16 40.691 -49.808 50.057 0.000 2.235 46 ATOM 46 CE LYS 16 40.325 -50.719 51.229 0.250 2.235 47 ATOM 47 NZ LYS 16 41.476 -50.882 52.125 -0.300 1.650 48 ATOM 48 HZ1 LYS 16 41.792 -49.942 52.438 0.350 0.600 49 ATOM 49 HZ2 LYS 16 42.250 -51.355 51.617 0.350 0.600 [all …]
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/examples/hca-bind/UHBD/ |
H A D | bindf1.qcd | 55 ATOM 6 LYS N 9.128 -11.197 11.327 -.400 1.800 56 ATOM 6 LYS H 9.107 -11.710 10.469 .250 .800 57 ATOM 6 LYS CA 10.081 -11.543 12.414 .100 1.800 58 ATOM 6 LYS CB 10.880 -12.845 12.195 .000 1.800 59 ATOM 6 LYS CG 11.098 -13.428 13.623 .000 1.800 60 ATOM 6 LYS CD 11.930 -14.633 13.774 .000 1.800 61 ATOM 6 LYS CE 11.843 -15.247 15.204 .250 1.800 62 ATOM 6 LYS NZ 12.715 -16.480 15.228 -.300 1.800 63 ATOM 6 LYS HZ1 13.654 -16.248 14.845 .350 .800 64 ATOM 6 LYS HZ2 12.278 -17.225 14.648 .350 .800 [all …]
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/examples/hca-bind/ |
H A D | complex.pqr | 55 ATOM 55 N LYS 6 9.128 -11.197 11.327 -0.400 1.800 56 ATOM 56 H LYS 6 9.107 -11.710 10.469 0.250 0.800 57 ATOM 57 CA LYS 6 10.081 -11.543 12.414 0.100 1.800 58 ATOM 58 CB LYS 6 10.880 -12.845 12.195 0.000 1.800 59 ATOM 59 CG LYS 6 11.098 -13.428 13.623 0.000 1.800 60 ATOM 60 CD LYS 6 11.930 -14.633 13.774 0.000 1.800 61 ATOM 61 CE LYS 6 11.843 -15.247 15.204 0.250 1.800 63 ATOM 63 HZ1 LYS 6 13.654 -16.248 14.845 0.350 0.800 64 ATOM 64 HZ2 LYS 6 12.278 -17.225 14.648 0.350 0.800 65 ATOM 65 HZ3 LYS 6 12.813 -16.816 16.207 0.350 0.800 [all …]
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