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Searched refs:LYS (Results 1 – 25 of 539) sorted by relevance

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/dports/science/plumed/plumed2-2.7.2/user-doc/tutorials/old_tutorials/belfast-9a/system/
H A Dconf.gro60 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 …]
H A Dout.gro60 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 …]
H A Dem.gro60 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 …]
H A Dtopol.top93 ; 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 …]
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/tests/complete-test/
H A Dtest-output-1AFS-ph-low-ph-correct.propka1071 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 …]
H A Dtest-output-1AFS-ph-neutral-correct.propka1071 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 …]
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/sg/examples/data/pqr/
H A Dfig001_asc.pqr36 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 …]
/dports/science/py-MDAnalysisTests/MDAnalysisTests-0.19.2/MDAnalysisTests/data/
H A Dnamd_cgenff.psf26 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 …]
H A Dadk_open.pqr187 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 …]
H A Dadk_open.crd179 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 …]
/dports/science/plumed/plumed2-2.7.2/user-doc/tutorials/lugano-6d/
H A DGB1_start.gro30 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 …]
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/contrib/iapbs/modules/Amber/test/pbsa_pgb/iAPBS/
H A Dpgb.pqr62 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 …]
H A Dpgb-amber.pqr62 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 …]
H A Dpgb-parse.pqr62 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 …]
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/examples/bem/test_proteins/
H A D451c.pqr114 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 …]
/dports/biology/molden/molden5.8/test/
H A Dpdb.test69 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 …]
/dports/science/gromacs/gromacs-2021.4/src/gromacs/trajectoryanalysis/tests/
H A Dlysozyme.gro3 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 …]
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/pb_s_am/pbam/pbam_test_files/gtest/
H A Dtest.pqr21 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 …]
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/pb_s_am/pbsam/pbsam_test_files/gtest/
H A Dtest.pqr21 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 …]
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/examples/pka-lig/
H A Dbx6_7_bin_apbs.pqr40 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 …]
H A Dbx6_7_apo_apbs.pqr40 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 …]
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/tools/matlab/solver/Examples/pka/
H A Dbx6_7_apo_apbs.pqr40 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 …]
H A Dbx6_7_bin_apbs.pqr40 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 …]
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/examples/hca-bind/UHBD/
H A Dbindf1.qcd55 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 …]
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/examples/hca-bind/
H A Dcomplex.pqr55 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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