Generate INPHARMA-files

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The INPHARMA calculations depend on the following files:

hlist file
a text file specifying the non-exchangable protons in the PDB file
asgn file
a text file specifying visible peaks in the NMR-spectrum
vols file
a text file specifying the intensities of the NOEs

Below is a description for how to generate these files:

hlist files

Generating the hlist files is done with the program SpInpharma-hlist:

SpInpharma-hlist pdb D off ../02_structures/LL1.pdb > LL1.hlist
SpInpharma-hlist pdb D off ../02_structures/M77.pdb > M77.hlist
SpInpharma-hlist pdb D off ../02_structures/receptor.pdb > receptor_CH3.hlist


To avoid the methyl group treatment you can

#!/bin/bash
while read line
  do 
  if [[ "$line" == *type* ]]; then
      if [[ "$line" == *CH3* ]]; then
	  atoms=`echo $line | cut -d "[" -f2 | cut -d "]" -f1`
	  IFS=',' read -a array <<< "$atoms"
	  echo '  {"type": "H", "ids": ['${array[0]}'], "S": 1.00},'
	  echo '  {"type": "H", "ids": ['${array[1]}'], "S": 1.00},'
	  echo '  {"type": "H", "ids": ['${array[2]}'], "S": 1.00},'
      else
	  echo "  "$line
      fi
  else
      echo $line
  fi
done < "receptor_CH3.hlist"

asgn files

The asignment files needs to be generated manually based on your NMR data and the visible protons. For each ligand-pair two asgn files needs to be created.

The first file specifies which protons belongs to each group. E.g. in the example file below, atom numbers 4946 and 4949 have overlapping chemical shifts. Thus, these two protons are in the same group and can be named LL1-1_2.

The asgn files for the INPHARMA experiment LL1-M77 have the following .asgn files:

LL1-M77.asgn:

{
 "LL1-1_2": [4946, 4949],
 "LL1-3_4": [4944, 4951],
 "LL1-5":   [4929],
 "LL1-6":   [4931],
 "LL1-7":   [4933],
 "LL1-8":   [4935]
}

M77-LL1.asgn:

{
 "M77-1_4":  [4937,4938,4933,4932],
 "M77-2":    [4941,4940],
 "M77-3":    [4944,4943],
 "M77-5":    [4930,4931],
 "M77-6":    [4959],
 "M77-7_11": [4961,4951],
 "M77-8":    [4964],
 "M77-9":    [4955],
 "M77-10":   [4953]
}

Peak list (.vols) files

{
  "spectrometer_freq": 800,
  "conc_receptor": 28.0,
  "conc_l1": 250.0,
  "conc_l2": 250.0,
  "mixing_times": [0.3, 0.5, 0.7],
  "integrals_mode": "abs",
  "normalization": "diag",
  "peaks": [
   {"F2": "LL1-1_2",    "F1": "LL1-1_2",     "integrals": [    [29965150000.0, 1],   [21556880000.0, 1],   [15692360000.0, 1]   ]},
   {"F2": "LL1-1_2",    "F1": "M77-10",      "integrals": [        [9686894.0, 1],      [36833380.0, 1],      [56290816.0, 1]   ]},
   {"F2": "LL1-3_4",    "F1": "LL1-3_4",     "integrals": [    [19873240000.0, 1],   [13063190000.0, 1],    [8850376000.0, 1]   ]},
   {"F2": "LL1-3_4",    "F1": "M77-1_4",     "integrals": [       [29175031.0, 1],      [73157068.0, 1],     [102993032.0, 1]   ]},
   {"F2": "LL1-3_4",    "F1": "M77-3",       "integrals": [       [47171620.0, 1],      [93144924.0, 1],     [102726224.0, 1]   ]},
   {"F2": "LL1-3_4",    "F1": "M77-5",       "integrals": [       [59633089.0, 1],      [66627240.0, 1],     [118633070.0, 1]   ]},
   {"F2": "LL1-3_4",    "F1": "M77-7_11",    "integrals": [       [80441240.0, 1],     [129055416.0, 1],     [172713952.0, 1]   ]},
   {"F2": "LL1-3_4",    "F1": "M77-8",       "integrals": [       [10756400.0, 1],      [35942800.0, 1],      [44588360.0, 1]   ]},
   {"F2": "LL1-5",      "F1": "LL1-5",       "integrals": [    [13643270000.0, 1],    [9301160000.0, 1],    [6410786000.0, 1]   ]},
   {"F2": "LL1-5",      "F1": "M77-5",       "integrals": [       [22077790.0, 1],      [37571734.0, 1],      [38576120.0, 1]   ]},
   {"F2": "LL1-5",      "F1": "M77-7_11",    "integrals": [       [20394940.0, 1],      [38536060.0, 1],      [59385460.0, 1]   ]},
   {"F2": "LL1-5",      "F1": "M77-8",       "integrals": [       [23185010.0, 1],      [39938332.0, 1],      [56298380.0, 1]   ]},
   {"F2": "LL1-5",      "F1": "M77-9",       "integrals": [       [28881680.0, 1],      [35679300.0, 1],      [62475760.0, 1]   ]},
   {"F2": "LL1-6",      "F1": "LL1-6",       "integrals": [     [6835483000.0, 1],    [4157135000.0, 1],    [2624350000.0, 1]   ]},
   {"F2": "LL1-6",      "F1": "M77-10",      "integrals": [       [50794144.0, 1],      [61428420.0, 1],      [74932048.0, 1]   ]},
   {"F2": "LL1-6",      "F1": "M77-7_11",    "integrals": [       [42063000.0, 1],      [81922880.0, 1],     [102147248.0, 1]   ]},
   {"F2": "LL1-7",      "F1": "LL1-7",       "integrals": [     [8910534000.0, 1],    [5131341000.0, 1],    [3083549000.0, 1]   ]},
   {"F2": "LL1-7",      "F1": "M77-10",      "integrals": [       [23264870.0, 1],      [29621950.0, 1],      [44214108.0, 1]   ]},
   {"F2": "LL1-7",      "F1": "M77-7_11",    "integrals": [       [36178980.0, 1],      [56264876.0, 1],      [76717680.0, 1]   ]},
   {"F2": "LL1-8",      "F1": "LL1-8",       "integrals": [     [7415932000.0, 1],    [4098660000.0, 1],    [2352871000.0, 1]   ]},
   {"F2": "LL1-8",      "F1": "M77-1_4",     "integrals": [       [28899700.0, 1],      [44743610.0, 1],      [67072660.0, 1]   ]},
   {"F2": "LL1-8",      "F1": "M77-2",       "integrals": [        [8452066.0, 1],      [19188918.0, 1],      [29461802.0, 1]   ]},
   {"F2": "LL1-8",      "F1": "M77-3",       "integrals": [       [40145780.0, 1],      [56795068.0, 1],      [71525448.0, 1]   ]},
   {"F2": "LL1-8",      "F1": "M77-5",       "integrals": [       [43323671.0, 1],      [71287512.0, 1],      [85734058.0, 1]   ]},
   {"F2": "LL1-8",      "F1": "M77-7_11",    "integrals": [      [117528400.0, 1],     [130700200.0, 1],     [140076288.0, 1]   ]},
   {"F2": "LL1-8",      "F1": "M77-8",       "integrals": [        [6992107.0, 1],       [7987513.0, 1],      [25548920.0, 1]   ]},
   {"F2": "M77-10",     "F1": "LL1-3_4",     "integrals": [       [34577780.0, 1],      [48750180.0, 1],      [48458548.0, 1]   ]},
   {"F2": "M77-10",     "F1": "LL1-5",       "integrals": [       [60730708.0, 1],      [49952508.0, 1],      [54327332.0, 1]   ]},
   {"F2": "M77-10",     "F1": "LL1-7",       "integrals": [       [17635350.0, 1],      [27196402.0, 1],      [39696712.0, 1]   ]},
   {"F2": "M77-10",     "F1": "LL1-8",       "integrals": [       [26259440.0, 1],      [21158580.0, 1],      [31358140.0, 1]   ]},
   {"F2": "M77-10",     "F1": "M77-10",      "integrals": [    [13486830000.0, 1],    [9320196000.0, 1],    [6465244000.0, 1]   ]},
   {"F2": "M77-1_4",    "F1": "LL1-7",       "integrals": [              [0.0, 0],             [0.0, 0],      [42791420.0, 1]   ]},
   {"F2": "M77-1_4",    "F1": "M77-1_4",     "integrals": [    [75538450000.0, 1],   [51252550000.0, 1],   [34869950000.0, 1]   ]},
   {"F2": "M77-2",      "F1": "LL1-3_4",     "integrals": [       [19805630.0, 1],      [28366170.0, 1],      [33999300.0, 1]   ]},
   {"F2": "M77-2",      "F1": "LL1-8",       "integrals": [              [0.0, 0],      [17632020.0, 1],      [23959870.0, 1]   ]},
   {"F2": "M77-2",      "F1": "M77-2",       "integrals": [    [36983700000.0, 1],   [23752270000.0, 1],   [15344660000.0, 1]   ]},
   {"F2": "M77-3",      "F1": "LL1-3_4",     "integrals": [       [23183820.0, 1],      [57810712.0, 1],      [72900024.0, 1]   ]},
   {"F2": "M77-3",      "F1": "LL1-5",       "integrals": [       [11789810.0, 1],      [24577240.0, 1],      [27179420.0, 1]   ]},
   {"F2": "M77-3",      "F1": "LL1-6",       "integrals": [              [0.0, 0],      [24962240.0, 1],      [21280460.0, 1]   ]},
   {"F2": "M77-3",      "F1": "LL1-8",       "integrals": [       [29141160.0, 1],      [49085252.0, 1],      [52614732.0, 1]   ]},
   {"F2": "M77-3",      "F1": "M77-3",       "integrals": [    [27377330000.0, 1],   [17173270000.0, 1],   [10829660000.0, 1]   ]},
   {"F2": "M77-5",      "F1": "LL1-3_4",     "integrals": [       [40262512.0, 1],      [63863896.0, 1],      [69823464.0, 1]   ]},
   {"F2": "M77-5",      "F1": "LL1-8",       "integrals": [       [35002248.0, 1],      [54774560.0, 1],      [51758808.0, 1]   ]},
   {"F2": "M77-5",      "F1": "M77-5",       "integrals": [    [28522030000.0, 1],   [17557330000.0, 1],   [10957470000.0, 1]   ]},
   {"F2": "M77-6",      "F1": "LL1-3_4",     "integrals": [      [110170184.0, 1],     [194557712.0, 1],     [207236800.0, 1]   ]},
   {"F2": "M77-6",      "F1": "LL1-5",       "integrals": [       [29691330.0, 1],      [27812090.0, 1],      [39287000.0, 1]   ]},
   {"F2": "M77-6",      "F1": "LL1-7",       "integrals": [       [22012070.0, 1],      [53755464.0, 1],      [66701256.0, 1]   ]},
   {"F2": "M77-6",      "F1": "LL1-8",       "integrals": [       [53937560.0, 1],      [86359416.0, 1],     [105129896.0, 1]   ]},
   {"F2": "M77-6",      "F1": "M77-6",       "integrals": [    [21034340000.0, 1],   [15649650000.0, 1],   [11689540000.0, 1]   ]},
   {"F2": "M77-7_11",   "F1": "LL1-3_4",     "integrals": [       [84930272.0, 1],     [132054496.0, 1],     [181672800.0, 1]   ]},
   {"F2": "M77-7_11",   "F1": "LL1-5",       "integrals": [       [31280980.0, 1],      [40168460.0, 1],      [51793760.0, 1]   ]},
   {"F2": "M77-7_11",   "F1": "LL1-6",       "integrals": [       [30937592.0, 1],      [36724268.0, 1],      [46311872.0, 1]   ]},
   {"F2": "M77-7_11",   "F1": "LL1-7",       "integrals": [       [31649030.0, 1],      [76905736.0, 1],      [95287784.0, 1]   ]},
   {"F2": "M77-7_11",   "F1": "LL1-8",       "integrals": [      [132659000.0, 1],     [161061408.0, 1],     [178518592.0, 1]   ]},
   {"F2": "M77-7_11",   "F1": "M77-7_11",    "integrals": [    [21505780000.0, 1],   [14769930000.0, 1],   [10229090000.0, 1]   ]},
   {"F2": "M77-8",      "F1": "LL1-3_4",     "integrals": [       [24649140.0, 1],      [41926800.0, 1],      [57480432.0, 1]   ]},
   {"F2": "M77-8",      "F1": "M77-8",       "integrals": [    [20564240000.0, 1],   [15322420000.0, 1],   [11440420000.0, 1]   ]},
   {"F2": "M77-9",      "F1": "LL1-3_4",     "integrals": [       [10537970.0, 1],      [13115120.0, 1],      [33131510.0, 1]   ]},
   {"F2": "M77-9",      "F1": "LL1-5",       "integrals": [       [13613220.0, 1],      [29664778.0, 1],      [44733740.0, 1]   ]},
   {"F2": "M77-9",      "F1": "LL1-6",       "integrals": [       [20774340.0, 1],      [33102720.0, 1],      [36172380.0, 1]   ]},
   {"F2": "M77-9",      "F1": "LL1-7",       "integrals": [       [14838710.0, 1],      [26831902.0, 1],      [30650028.0, 1]   ]},
   {"F2": "M77-9",      "F1": "LL1-8",       "integrals": [              [0.0, 0],      [11702840.0, 1],      [20931100.0, 1]   ]},
   {"F2": "M77-9",      "F1": "M77-9",       "integrals": [    [16197590000.0, 1],   [11357670000.0, 1],    [8042287000.0, 1]   ]}
]
}