{"id":883,"date":"2019-04-17T21:14:56","date_gmt":"2019-04-17T21:14:56","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/crankpep\/?page_id=883"},"modified":"2019-06-11T21:04:27","modified_gmt":"2019-06-11T21:04:27","slug":"tutorial-cyclic","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/adcp\/tutorial-cyclic\/","title":{"rendered":"Tutorial Cyclic Peptide"},"content":{"rendered":"<p class=\"last-modified\">This page was last updated on June 11th, 2019 at 09:04 pm<\/p><div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-1 nonhundred-percent-fullwidth non-hundred-percent-height-scrolling\" style=\"--awb-border-radius-top-left:0px;--awb-border-radius-top-right:0px;--awb-border-radius-bottom-right:0px;--awb-border-radius-bottom-left:0px;--awb-flex-wrap:wrap;\" ><div class=\"fusion-builder-row fusion-row\"><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-0 fusion_builder_column_1_1 1_1 fusion-one-full fusion-column-first fusion-column-last\" style=\"--awb-bg-size:cover;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\"><div class=\"fusion-text fusion-text-1\"><h3>A redocking tutorial for docking peptides with disulfide bond<\/h3>\n<p>In this tutorial we illustrate how to re-dock a cyclic peptide into its native receptor.\u00a0We will redock a <span id=\"structureTitle\">10-mer peptide from EBV into HLA-A1101 (<a href=\"https:\/\/www.rcsb.org\/structure\/5GRD\">PDB: 5GRD<\/a>).<\/span><\/p>\n<p><strong>In this tutorial you will learn<\/strong>:<\/p>\n<ul>\n<li>to generate a target file for a docking in a box defined by the known peptide.<\/li>\n<li>to run <i>ADCP\u00a0<\/i>to re-dock the cyclic peptides<\/li>\n<li>to understand the output of an <i>ADCP\u00a0<\/i>docking run<\/li>\n<\/ul>\n<p><strong>Prerequisites<\/strong>:<\/p>\n<ul>\n<li>You have\u00a0<a href=\"https:\/\/ccsb.scripps.edu\/adcp\/downloads\/\">downloaded and installed the ADFRsuite 1.0<\/a><\/li>\n<li>ADFRsuite-1.0\/bin in in your path\u00a0(if you use a command shell in Max OS, or Linux)<\/li>\n<li>you have downloaded and unzipped the\u00a0<a href=\"https:\/\/ccsb.scripps.edu\/adcp\/download\/1063\/\">data file associated with this tutorial<\/a>.<\/li>\n<\/ul>\n<h2>Go back to <a href=\"http:\/\/ccsb.scripps.edu\/adcp\">ADCP Homepage<\/a>.<\/h2>\n<\/div><div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-separator fusion-full-width-sep\" style=\"margin-left: auto;margin-right: auto;margin-top:15px;margin-bottom:25px;width:100%;\"><div class=\"fusion-separator-border sep-shadow\" style=\"--awb-height:20px;--awb-amount:20px;background:radial-gradient(ellipse at 50% -50% , #e0dede 0px, rgba(255, 255, 255, 0) 80%) repeat scroll 0 0 rgba(0, 0, 0, 0);background:-webkit-radial-gradient(ellipse at 50% -50% , #e0dede 0px, rgba(255, 255, 255, 0) 80%) repeat scroll 0 0 rgba(0, 0, 0, 0);background:-moz-radial-gradient(ellipse at 50% -50% , #e0dede 0px, rgba(255, 255, 255, 0) 80%) repeat scroll 0 0 rgba(0, 0, 0, 0);background:-o-radial-gradient(ellipse at 50% -50% , #e0dede 0px, rgba(255, 255, 255, 0) 80%) repeat scroll 0 0 rgba(0, 0, 0, 0);\"><\/div><\/div><div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-tabs fusion-tabs-1 clean vertical-tabs icon-position-left mobile-mode-accordion\" style=\"--awb-title-border-radius-top-left:0px;--awb-title-border-radius-top-right:0px;--awb-title-border-radius-bottom-right:0px;--awb-title-border-radius-bottom-left:0px;--awb-inactive-color:#9acae0;--awb-background-color:#ffffff;--awb-border-color:#9acae0;--awb-active-border-color:#d65169;\"><div class=\"nav\"><ul class=\"nav-tabs\" role=\"tablist\"><li class=\"active\" role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-3237c8ae924013299c3\" aria-selected=\"true\" id=\"fusion-tab-generatetargetfile\" href=\"#tab-3237c8ae924013299c3\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-cogs fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Generate target file<\/h4><\/a><\/li><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-58a67de6ba68b4669e3\" aria-selected=\"false\" tabindex=\"-1\" id=\"fusion-tab-dockingthecyclicpeptide\" href=\"#tab-58a67de6ba68b4669e3\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-cogs fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Docking the cyclic peptide<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-content\"><div class=\"nav fusion-mobile-tab-nav\"><ul class=\"nav-tabs\" role=\"tablist\"><li class=\"active\" role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-3237c8ae924013299c3\" aria-selected=\"true\" id=\"mobile-fusion-tab-generatetargetfile\" href=\"#tab-3237c8ae924013299c3\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-cogs fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Generate target file<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix in active\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-generatetargetfile\" id=\"tab-3237c8ae924013299c3\">\n<h4>Generate the target file containing the affinity maps.<\/h4>\n<p>First lets go to the directory for this tutorial.<\/p>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-1 > .CodeMirror, .fusion-syntax-highlighter-1 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}.fusion-syntax-highlighter-1 > .CodeMirror .CodeMirror-gutters { background-color: var(--awb-color2); }.fusion-syntax-highlighter-1 > .CodeMirror .CodeMirror-linenumber { color: var(--awb-color8); }<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-1 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><div class=\"syntax-highlighter-copy-code\"><span class=\"syntax-highlighter-copy-code-title\" data-id=\"fusion_syntax_highlighter_1\" style=\"font-size:14px;\">Copy to Clipboard<\/span><\/div><label for=\"fusion_syntax_highlighter_1\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_1\" data-readOnly=\"nocursor\" data-lineNumbers=\"1\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/x-sh\">cd ADCP_tutorial_data\/5GRD<\/textarea><\/div>\n<p>For this tutorial, we will start directly from the PDBQT files. Please refer to the <a href=\"https:\/\/ccsb.scripps.edu\/adcp\/tutorial-redocking\/\">first tutorial<\/a> on how to converting PDB files to PDBQT files.<\/p>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-2 > .CodeMirror, .fusion-syntax-highlighter-2 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}.fusion-syntax-highlighter-2 > .CodeMirror .CodeMirror-gutters { background-color: var(--awb-color2); }.fusion-syntax-highlighter-2 > .CodeMirror .CodeMirror-linenumber { color: var(--awb-color8); }<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-2 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><div class=\"syntax-highlighter-copy-code\"><span class=\"syntax-highlighter-copy-code-title\" data-id=\"fusion_syntax_highlighter_2\" style=\"font-size:14px;\">Copy to Clipboard<\/span><\/div><label for=\"fusion_syntax_highlighter_2\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_2\" data-readOnly=\"nocursor\" data-lineNumbers=\"1\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/x-sh\">agfr -r 5GRD_recH.pdbqt -l 5GRD_pepH.pdbqt -o 5GRD<\/textarea><\/div>\n<p>The command produces the following output:<\/p>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-3 > .CodeMirror, .fusion-syntax-highlighter-3 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}.fusion-syntax-highlighter-3 > .CodeMirror .CodeMirror-gutters { background-color: var(--awb-color2); }.fusion-syntax-highlighter-3 > .CodeMirror .CodeMirror-linenumber { color: var(--awb-color8); }<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-3 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><div class=\"syntax-highlighter-copy-code\"><span class=\"syntax-highlighter-copy-code-title\" data-id=\"fusion_syntax_highlighter_3\" style=\"font-size:14px;\">Copy to Clipboard<\/span><\/div><label for=\"fusion_syntax_highlighter_3\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_3\" data-readOnly=\"nocursor\" data-lineNumbers=\"1\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/html\">MSMSLIB 1.4.4 started on ambae\nCopyright M.F. Sanner (March 2000)\nCompilation flags  \n#################################################################\n# If you used AGFR in your work, please cite:                   #\n#                                                               #\n# P.A. Ravindranath S. Forli, D.S. Goodsell, A.J. Olson and     #\n# M.F. Sanner                                                   #\n# AutoDockFR: Advances in Protein-Ligand Docking with           #\n# Explicitly Specified Binding Site Flexibility                 #\n# PLoS Comput Biol 11(12): e1004586                             #\n# DOI:10.1371\/journal.pcbi.1004586                              #\n#                                                               #\n# P. Ananad Ravindranath and M.F. Sanner                        #\n# AutoSite: an automated approach for pseudoligands prediction  #\n# - From ligand binding sites identification to predicting key  #\n# ligand atoms                                                  #\n# Bioinformatics (2016)                                         #\n# DOI:10.1093\/bioinformatics\/btw367                             #\n#                                                               #\n# Please see http:\/\/adfr.scripps.edu for more information.      #\n#################################################################\n\nComputing grids on ambae a Linux-4.15.0-47-generic-x86_64-with-debian-buster-sid computer\nDate Mon Jun  3 16:54:32 2019\n\nloading receptor: 5GRD_recH.pdbqt\nloading ligand: 5GRD_pepH.pdbqt\n\nset box using ligand\n    Box center:    29.694   -16.993    -4.930\n    Box length:    24.750    33.750    19.500\n    Box size  :        66        90        52\n    padding   :     4.000\n    spacing   :     0.375\n\nidentifying pockets using AutoSite ....\nScanning at: -0.36 -0.792 -0.6\nclust.| Energy| # of |Rad. of | energy |   bns    |score   |\nnumber|       |points|gyration|per vol.|buriedness|v*b^2\/rg|\n------+-------+------+--------+--------+----------+--------|\n    1   -39.92    73    3.10    -0.55     0.885     18.48 \nScanning at: -0.315 -0.693 -0.525\nclust.| Energy| # of |Rad. of | energy |   bns    |score   |\nnumber|       |points|gyration|per vol.|buriedness|v*b^2\/rg|\n------+-------+------+--------+--------+----------+--------|\n    1   -53.04    82    2.87    -0.65     0.907     23.49 \n    2   -50.19    90    3.24    -0.56     0.890     22.01 \nScanning at: -0.27 -0.594 -0.45\nclust.| Energy| # of |Rad. of | energy |   bns    |score   |\nnumber|       |points|gyration|per vol.|buriedness|v*b^2\/rg|\n------+-------+------+--------+--------+----------+--------|\n    1  -170.26   313    6.04    -0.54     0.801     33.26 \n    2   -95.79   169    4.19    -0.57     0.815     26.77 \n    3   -47.08    85    3.15    -0.55     0.684     12.61 \nScanning at: -0.225 -0.495 -0.375\nclust.| Energy| # of |Rad. of | energy |   bns    |score   |\nnumber|       |points|gyration|per vol.|buriedness|v*b^2\/rg|\n------+-------+------+--------+--------+----------+--------|\n    1  -489.13   973   10.33    -0.50     0.739     51.37 \n    2   -32.07    54    2.10    -0.59     0.720     13.35 \n    found 4 pocket(s)\n\n    pocket|  energy | # of |Rad. of | energy |   bns    | score  \n    number|         |points|gyration|per vol.|buriedness|v*b^2\/rg\n    ------+---------+------+--------+--------+----------+---------\n        1   -208.12   447    6.30     -0.47      0.84      49.87\n        2   -118.34   237    4.75     -0.50      0.88      38.23\n        3    -45.77    97    2.82     -0.47      0.83      23.59\n        4    -59.14   122    3.62     -0.48      0.82      22.42\n    merging clusters ...\ndone. got 119 fill Points, in 5.96 (sec)\n\nsetting map types using: all to ['HS', 'Mg', 'HD', 'NA', 'Fe', 'Br', 'NS', 'A', 'C', 'Mn', 'G', 'F', 'I', 'H', 'J', 'N', 'Q', 'P', 'S', 'GA', 'Z', 'Zn', 'Cl', 'Ca', 'OA', 'SA', 'OS']\n\ncomputing maps for center=(29.694 -16.993 -4.930) size=(24.750 33.750 19.500) dims=(66 90 52) ...\n    113 points inside the box\n\n    maps computed in 4.07 (sec)\nmaking target file 5GRD.trg ...done.\n    done. 9.11 (sec)\n<\/textarea><\/div>\n<\/div><div class=\"nav fusion-mobile-tab-nav\"><ul class=\"nav-tabs\" role=\"tablist\"><li role=\"presentation\"><a class=\"tab-link\" data-toggle=\"tab\" role=\"tab\" aria-controls=\"tab-58a67de6ba68b4669e3\" aria-selected=\"false\" tabindex=\"-1\" id=\"mobile-fusion-tab-dockingthecyclicpeptide\" href=\"#tab-58a67de6ba68b4669e3\"><h4 class=\"fusion-tab-heading\"><i class=\"fontawesome-icon fa-cogs fas\" aria-hidden=\"true\" style=\"font-size:13px;\"><\/i>Docking the cyclic peptide<\/h4><\/a><\/li><\/ul><\/div><div class=\"tab-pane fade fusion-clearfix\" role=\"tabpanel\" tabindex=\"0\" aria-labelledby=\"fusion-tab-dockingthecyclicpeptide\" id=\"tab-58a67de6ba68b4669e3\">\n<h4><span style=\"color: #000000;\">Perform the docking<\/span><\/h4>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-4 > .CodeMirror, .fusion-syntax-highlighter-4 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}.fusion-syntax-highlighter-4 > .CodeMirror .CodeMirror-gutters { background-color: var(--awb-color2); }.fusion-syntax-highlighter-4 > .CodeMirror .CodeMirror-linenumber { color: var(--awb-color8); }<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-4 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><div class=\"syntax-highlighter-copy-code\"><span class=\"syntax-highlighter-copy-code-title\" data-id=\"fusion_syntax_highlighter_4\" style=\"font-size:14px;\">Copy to Clipboard<\/span><\/div><label for=\"fusion_syntax_highlighter_4\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_4\" data-readOnly=\"nocursor\" data-lineNumbers=\"1\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/x-sh\">adcp -t 5GRD.trg -s sscsscplsk -N 20 -n 500000 -cys -o 5GRD_redocking -ref 5GRD_pepH.pdbqt -nc 0.8<\/textarea><\/div>\n<div class=\"fusion-sep-clear\"><\/div><div class=\"fusion-separator fusion-full-width-sep\" style=\"margin-left: auto;margin-right: auto;margin-top:15px;margin-bottom:15px;width:100%;\"><div class=\"fusion-separator-border sep-double sep-solid\" style=\"--awb-height:20px;--awb-amount:20px;border-color:#e0dede;border-top-width:1px;border-bottom-width:1px;\"><\/div><\/div><div class=\"fusion-sep-clear\"><\/div>\n<p>Note we added two options compared with redocking the linear peptide.<\/p>\n<p>-cys\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 enables the potential for disulfide bond.<\/p>\n<p>-nc 0.8\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 use native contacts as clustering criteria. We recommend using native contacts for larger peptides.<\/p>\n<p>This calculation generates the following files:<\/p>\n<ul>\n<li>5GRD_redocking_ranked_.pdb\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0\u00a0\u00a0 # the final solutions with ranking after clustering<\/li>\n<li>5GRD_redocking_.pdb\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0# the MC trajectory for each replica<\/li>\n<li>5GRD_redocking_.out\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 # detailed output file for each replica<\/li>\n<\/ul>\n<p>An example output is listed below:<\/p>\n<style type=\"text\/css\" scopped=\"scopped\">.fusion-syntax-highlighter-5 > .CodeMirror, .fusion-syntax-highlighter-5 > .CodeMirror .CodeMirror-gutters {background-color:var(--awb-color1);}.fusion-syntax-highlighter-5 > .CodeMirror .CodeMirror-gutters { background-color: var(--awb-color2); }.fusion-syntax-highlighter-5 > .CodeMirror .CodeMirror-linenumber { color: var(--awb-color8); }<\/style><div class=\"fusion-syntax-highlighter-container fusion-syntax-highlighter-5 fusion-syntax-highlighter-theme-light\" style=\"opacity:0;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font-size:14px;border-width:1px;border-style:solid;border-color:var(--awb-color3);\"><div class=\"syntax-highlighter-copy-code\"><span class=\"syntax-highlighter-copy-code-title\" data-id=\"fusion_syntax_highlighter_5\" style=\"font-size:14px;\">Copy to Clipboard<\/span><\/div><label for=\"fusion_syntax_highlighter_5\" class=\"screen-reader-text\">Syntax Highlighter<\/label><textarea class=\"fusion-syntax-highlighter-textarea\" id=\"fusion_syntax_highlighter_5\" data-readOnly=\"nocursor\" data-lineNumbers=\"1\" data-lineWrapping=\"\" data-theme=\"default\" data-mode=\"text\/html\">Detected 8 cores, using 8 cores\nusing ramaprob.data in current folder\nPerforming search (20 ADCP runs with 5000000 steps each) ...\n0%   10   20   30   40   50   60   70   80   90   100%\n|----|----|----|----|----|----|----|----|----|----|\nDocking performed in 687.79 seconds, i.e. 0 hours 11 minutes 27.785609 seconds \nfinish calculating neighbors for 2908 poses with 4.2 seconds\nmode |  affinity  | ref. | clust. | rmsd | energy | best |\n     | (kcal\/mol) | fnc  |  size  | stdv |  stdv  | run  |\n-----+------------+------+--------+------+--------+------+\n   1        -27.1    0.975      12      NA      NA    493 \n   2        -25.6    1.000       8      NA      NA    484 \n   3        -24.2    0.975       3      NA      NA    476 \n   4        -23.9    0.875      22      NA      NA    1967 \n   5        -23.4    0.925       3      NA      NA    472 \n   6        -22.6    0.825      30      NA      NA    468 \n   7        -22.3    0.775       4      NA      NA    1975 \n   8        -21.5    0.800       1      NA      NA    498 \n   9        -21.4    0.600      46      NA      NA    2540 \n  10        -21.3    0.825       4      NA      NA    1944 \n  11        -21.1    0.775       1      NA      NA    500 \n  12        -20.6    0.675      17      NA      NA    1940 \n  13        -20.4    0.675       1      NA      NA    1977 \n  14        -20.4    0.700      10      NA      NA    436 \n  15        -20.4    0.075      30      NA      NA    1562 \n  16        -20.3    0.725      12      NA      NA    1968 \n  17        -20.2    0.725       1      NA      NA    494 \n  18        -19.9    0.725       1      NA      NA    502 \n  19        -19.9    0.650       1      NA      NA    1973 \n  20        -19.8    0.750       1      NA      NA    1976 \n  21        -19.8    0.075      18      NA      NA    1400 \n  22        -19.8    0.075      14      NA      NA    2328 \n  23        -19.7    0.550       1      NA      NA    2544 \n  24        -19.4    0.075      47      NA      NA    2907 \n  25        -19.3    0.625       1      NA      NA    2545 \n  26        -19.2    0.100      29      NA      NA    2114 \n  27        -19.2    0.200      35      NA      NA    803 \n  28        -19.1    0.625       1      NA      NA    503 \n  29        -18.9    0.600       1      NA      NA    501 \n  30        -18.8    0.700       1      NA      NA    424 \n  31        -18.7    0.075       1      NA      NA    2123 \n  32        -18.7    0.375       8      NA      NA    1192 \n  33        -18.6    0.375      14      NA      NA    1179 \n  34        -18.6    0.025      34      NA      NA    1568 \n  35        -18.6    0.800       3      NA      NA    421 \n  36        -18.5    0.050      21      NA      NA    1384 \n  37        -18.5    0.475      11      NA      NA    2728 \n  38        -18.4    0.100      30      NA      NA    2323 \n  39        -18.3    0.725       4      NA      NA    417 \n  40        -18.3    0.675       1      NA      NA    448 \n  41        -18.2    0.800       4      NA      NA    1924 \n  42        -18.2    0.350      12      NA      NA    1169 \n  43        -18.0    0.375       7      NA      NA    1188 \n  44        -18.0    0.700      12      NA      NA    1903 \n  45        -18.0    0.375       3      NA      NA    1162 \n  46        -17.9    0.075       2      NA      NA    2119 \n  47        -17.7    0.150      24      NA      NA    138 \n  48        -17.7    0.675       1      NA      NA    1929 \n  49        -17.7    0.675       3      NA      NA    413 \n  50        -17.7    0.150      15      NA      NA    654 \n  51        -17.7    0.100       1      NA      NA    1405 \n  52        -17.7    0.375       2      NA      NA    1186 \n  53        -17.5    0.625       5      NA      NA    410 \n  54        -17.4    0.100       1      NA      NA    2122 \n  55        -17.3    0.475       3      NA      NA    2719 \n  56        -17.2    0.025      15      NA      NA    964 \n  57        -17.1    0.750       6      NA      NA    1889 \n  58        -17.0    0.050       1      NA      NA    954 \n  59        -16.9    0.375       1      NA      NA    2730 \n  60        -16.9    0.075       2      NA      NA    2322 \n  61        -16.8    0.600       1      NA      NA    434 \n  62        -16.7    0.600       1      NA      NA    2716 \n  63        -16.6    0.750       7      NA      NA    405 \n  64        -16.6    0.500       4      NA      NA    2715 \n  65        -16.3    0.350       2      NA      NA    1140 \n  66        -16.3    0.100       8      NA      NA    2082 \n  67        -16.3    0.675      10      NA      NA    398 \n  68        -16.3    0.750       1      NA      NA    465 \n  69        -16.2    0.375       1      NA      NA    1183 \n  70        -16.2    0.075       1      NA      NA    1408 \n  71        -16.2    0.475       2      NA      NA    2738 \n  72        -16.2    0.175      11      NA      NA    1749 \n  73        -16.1    0.050       7      NA      NA    1361 \n  74        -16.1    0.050       1      NA      NA    956 \n  75        -16.1    0.050       1      NA      NA    1571 \n  76        -16.1    0.300       1      NA      NA    1748 \n  77        -16.0    0.400       1      NA      NA    2737 \n  78        -16.0    0.575       4      NA      NA    1909 \n  79        -16.0    0.400       1      NA      NA    1167 \n  80        -16.0    0.450       9      NA      NA    2734 \n  81        -16.0    0.325       1      NA      NA    1181 \n  82        -16.0    0.475       1      NA      NA    2736 \n  83        -15.9    0.550       4      NA      NA    2488 \n  84        -15.8    0.050       2      NA      NA    938 \n  85        -15.8    0.350       1      NA      NA    2739 \n  86        -15.8    0.100       4      NA      NA    2851 \n  87        -15.8    0.175       7      NA      NA    648 \n  88        -15.8    0.100       4      NA      NA    2850 \n  89        -15.6    0.350       1      NA      NA    1744 \n  90        -15.6    0.700       1      NA      NA    1904 \n  91        -15.5    0.200       7      NA      NA    282 \n  92        -15.4    0.100       3      NA      NA    1353 \n  93        -15.4    0.375       5      NA      NA    1130 \n  94        -15.4    0.075       2      NA      NA    2273 \n  95        -15.4    0.025       1      NA      NA    2321 \n  96        -15.3    0.075       1      NA      NA    2319 \n  97        -15.3    0.525       1      NA      NA    2732 \n  98        -15.3    0.000       1      NA      NA    963 \n  99        -15.3    0.175       2      NA      NA    759 \n 100        -15.3    0.650       1      NA      NA    1923 \nclean up unzipped map files\n<\/textarea><\/div>\n<p>Please note that docking cyclic peptide is extremely challenging, and the purpose of this tutorial is only to show the usage of <em>ADCP<\/em>. We suggest using more replicas with more Monte Carlo steps for real production runs.<\/p>\n<\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div>\n","protected":false},"excerpt":{"rendered":"<p>This page was last updated on June 11th, 2019 at  [&#8230;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-883","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/pages\/883","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/comments?post=883"}],"version-history":[{"count":30,"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/pages\/883\/revisions"}],"predecessor-version":[{"id":1161,"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/pages\/883\/revisions\/1161"}],"wp:attachment":[{"href":"https:\/\/ccsb.scripps.edu\/adcp\/wp-json\/wp\/v2\/media?parent=883"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}