Моделируем комплекс фрагмента антитела (VHH домен) с панкреатической альфа-амилазой с помощью программы ZDOCK.
%%bash
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/preps/golovin/progs/lib
export PATH=${PATH}:/home/preps/golovin/progs/bin
Скачаем необходимые файлы:
%%bash
wget http://kodomo.cmm.msu.ru/~golovin/zdock/uniCHARMM
wget http://kodomo.cmm.msu.ru/~golovin/zdock/amylase.pdb
wget http://kodomo.cmm.msu.ru/~golovin/zdock/camelid.pdb
--2018-05-16 14:05:20-- http://kodomo.cmm.msu.ru/~golovin/zdock/uniCHARMM Resolving kodomo.cmm.msu.ru... 93.180.63.127 Connecting to kodomo.cmm.msu.ru|93.180.63.127|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 17376 (17K) Saving to: `uniCHARMM' 0K .......... ...... 100% 55.9M=0s 2018-05-16 14:05:20 (55.9 MB/s) - `uniCHARMM' saved [17376/17376] --2018-05-16 14:05:20-- http://kodomo.cmm.msu.ru/~golovin/zdock/amylase.pdb Resolving kodomo.cmm.msu.ru... 93.180.63.127 Connecting to kodomo.cmm.msu.ru|93.180.63.127|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 387504 (378K) [chemical/x-pdb] Saving to: `amylase.pdb' 0K .......... .......... .......... .......... .......... 13% 58.8M 0s 50K .......... .......... .......... .......... .......... 26% 62.7M 0s 100K .......... .......... .......... .......... .......... 39% 59.1M 0s 150K .......... .......... .......... .......... .......... 52% 68.2M 0s 200K .......... .......... .......... .......... .......... 66% 70.0M 0s 250K .......... .......... .......... .......... .......... 79% 66.8M 0s 300K .......... .......... .......... .......... .......... 92% 66.8M 0s 350K .......... .......... ........ 100% 56.1M=0.006s 2018-05-16 14:05:20 (63.7 MB/s) - `amylase.pdb' saved [387504/387504] --2018-05-16 14:05:20-- http://kodomo.cmm.msu.ru/~golovin/zdock/camelid.pdb Resolving kodomo.cmm.msu.ru... 93.180.63.127 Connecting to kodomo.cmm.msu.ru|93.180.63.127|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 73224 (72K) [chemical/x-pdb] Saving to: `camelid.pdb' 0K .......... .......... .......... .......... .......... 69% 62.6M 0s 50K .......... .......... . 100% 73.7M=0.001s 2018-05-16 14:05:20 (65.6 MB/s) - `camelid.pdb' saved [73224/73224]
Добавляем водороды в оба пдб-файла.
! pdb2gmx -f amylase.pdb -o amylase_h.pdb -p -ff gromos53a6 -ignh -water none
:-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description ------------------------------------------------------------ -f amylase.pdb Input Structure file: gro g96 pdb tpr etc. -o amylase_h.pdb Output Structure file: gro g96 pdb etc. -p topol.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Structure file: gro g96 pdb etc. Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -nice int 0 Set the nicelevel -chainsep enum id_or_ter Condition in PDB files when a new chain should be started (adding termini): id_or_ter, id_and_ter, ter, id or interactive -merge enum no Merge multiple chains into a single [moleculetype]: no, all or interactive -ff string gromos53a6 Force field, interactive by default. Use -h for information. -water enum none Water model to use: select, none, spc, spce, tip3p, tip4p or tip5p -[no]inter bool no Set the next 8 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool no Interactive termini selection, instead of charged (default) -[no]lys bool no Interactive lysine selection, instead of charged -[no]arg bool no Interactive arginine selection, instead of charged -[no]asp bool no Interactive aspartic acid selection, instead of charged -[no]glu bool no Interactive glutamic acid selection, instead of charged -[no]gln bool no Interactive glutamine selection, instead of neutral -[no]his bool no Interactive histidine selection, instead of checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -dist real 0.3 Maximum donor-acceptor distance for a H-bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on phenylalanine, tryptophane and tyrosine -[no]ignh bool yes Ignore hydrogen atoms that are in the coordinate file -[no]missing bool no Continue when atoms are missing, dangerous -[no]v bool no Be slightly more verbose in messages -posrefc real 1000 Force constant for position restraints -vsite enum none Convert atoms to virtual sites: none, hydrogens or aromatics -[no]heavyh bool no Make hydrogen atoms heavy -[no]deuterate bool no Change the mass of hydrogens to 2 amu -[no]chargegrp bool yes Use charge groups in the .rtp file -[no]cmap bool yes Use cmap torsions (if enabled in the .rtp file) -[no]renum bool no Renumber the residues consecutively in the output -[no]rtpres bool no Use .rtp entry names as residue names Using the Gromos53a6 force field in directory gromos53a6.ff Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading amylase.pdb... Read 3898 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 496 residues with 3898 atoms chain #res #atoms 1 'A' 495 3898 All occupancies are one Opening force field file /usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp Atomtype 1 Reading residue database... (gromos53a6) Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 108 Sorting it all out... Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb Processing chain 1 'A' (3898 atoms, 495 residues) Analysing hydrogen-bonding network for automated assignment of histidine protonation. 761 donors and 727 acceptors were found. There are 1112 hydrogen bonds Will use HISE for residue 15 Will use HISE for residue 101 Will use HISD for residue 201 Will use HISD for residue 215 Will use HISE for residue 299 Will use HISE for residue 305 Will use HISE for residue 331 Will use HISE for residue 386 Will use HISE for residue 491 Identified residue TYR2 as a starting terminus. Identified residue LEU496 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS15 CYS28 CYS70 MET82 CYS86 HIS101 MET102 NE2108 SG226 SG568 SD667 SG699 NE2817 SD824 CYS28 SG226 1.477 CYS70 SG568 2.005 2.128 MET82 SD667 1.264 0.664 1.475 CYS86 SG699 1.513 0.203 1.981 0.534 HIS101 NE2817 1.466 2.637 1.962 2.164 2.578 MET102 SD824 1.986 2.772 1.528 2.188 2.655 0.870 CYS103 SG831 2.123 3.077 1.577 2.469 2.979 1.037 0.737 CYS115 SG895 2.157 2.309 0.203 1.653 2.156 1.985 1.471 CYS119 SG923 2.402 3.163 1.363 2.518 3.043 1.469 0.923 CYS141 SG1096 2.888 4.102 3.204 3.640 4.040 1.497 1.749 CYS160 SG1242 2.772 3.997 3.205 3.558 3.941 1.420 1.753 MET178 SD1384 2.656 2.994 1.850 2.453 2.834 1.782 1.043 HIS201 NE21563 1.740 3.049 2.737 2.701 3.028 0.792 1.580 MET202 SD1570 1.804 2.720 2.352 2.331 2.649 0.825 1.111 HIS215 NE21676 2.642 2.416 2.317 2.122 2.258 2.423 2.034 MET274 SD2144 2.653 3.240 4.641 3.546 3.408 3.660 4.424 MET287 SD2255 1.849 2.658 3.493 2.682 2.706 2.091 2.739 HIS299 NE22352 0.536 1.992 2.086 1.692 2.008 1.065 1.743 HIS305 NE22402 1.473 2.809 3.217 2.711 2.898 2.036 2.850 MET328 SD2572 1.412 2.027 3.367 2.252 2.160 2.491 3.157 HIS331 NE22596 2.492 2.925 4.402 3.239 3.060 3.331 4.014 MET339 SD2662 0.507 1.636 2.455 1.598 1.730 1.845 2.456 CYS378 SG2970 1.529 1.356 2.560 1.545 1.497 2.917 3.271 CYS384 SG3017 1.340 1.315 2.498 1.476 1.456 2.742 3.127 HIS386 NE23036 1.257 0.955 2.517 1.270 1.126 2.699 3.069 MET394 SD3115 2.231 2.212 4.016 2.685 2.399 3.533 4.122 CYS450 SG3564 3.335 2.796 4.811 3.404 2.991 4.742 5.228 CYS462 SG3645 3.478 2.975 4.970 3.576 3.172 4.888 5.389 HIS491 NE23860 2.628 2.179 4.197 2.766 2.367 3.964 4.451 CYS103 CYS115 CYS119 CYS141 CYS160 MET178 HIS201 SG831 SG895 SG923 SG1096 SG1242 SD1384 NE21563 CYS115 SG895 1.515 CYS119 SG923 0.491 1.251 CYS141 SG1096 1.755 3.157 2.151 CYS160 SG1242 1.802 3.169 2.218 0.203 MET178 SD1384 1.689 1.750 1.635 2.374 2.384 HIS201 NE21563 1.711 2.771 2.183 1.277 1.117 2.360 MET202 SD1570 1.644 2.362 1.991 1.560 1.442 1.536 0.963 HIS215 NE21676 2.738 2.313 2.748 3.305 3.242 1.362 2.862 MET274 SD2144 4.540 4.803 4.922 4.537 4.358 5.048 3.318 MET287 SD2255 3.121 3.590 3.516 2.799 2.607 3.134 1.690 HIS299 NE22352 1.799 2.205 2.156 2.412 2.297 2.554 1.272 HIS305 NE22402 2.743 3.343 3.150 2.914 2.779 3.729 1.791 MET328 SD2572 3.385 3.522 3.729 3.596 3.426 3.691 2.323 HIS331 NE22596 4.314 4.545 4.689 4.169 3.976 4.438 2.974 MET339 SD2662 2.537 2.616 2.840 3.171 3.041 3.151 1.957 CYS378 SG2970 3.289 2.761 3.425 4.358 4.256 3.837 3.236 CYS384 SG3017 3.151 2.697 3.310 4.175 4.070 3.712 3.041 HIS386 NE23036 3.203 2.714 3.369 4.145 4.028 3.557 2.979 MET394 SD3115 4.341 4.196 4.630 4.718 4.551 4.578 3.443 CYS450 SG3564 5.444 5.005 5.662 6.024 5.865 5.594 4.755 CYS462 SG3645 5.589 5.165 5.811 6.160 6.000 5.774 4.887 HIS491 NE23860 4.730 4.381 4.970 5.214 5.051 4.783 3.955 MET202 HIS215 MET274 MET287 HIS299 HIS305 MET328 SD1570 NE21676 SD2144 SD2255 NE22352 NE22402 SD2572 HIS215 NE21676 1.936 MET274 SD2144 3.747 4.709 MET287 SD2255 1.755 2.839 2.285 HIS299 NE22352 1.539 2.768 2.768 1.792 HIS305 NE22402 2.481 3.921 2.025 2.016 1.238 MET328 SD2572 2.515 3.322 1.406 1.306 1.624 1.553 HIS331 NE22596 3.161 3.913 1.193 1.475 2.632 2.349 1.118 MET339 SD2662 2.180 3.077 2.197 1.837 0.796 1.173 1.088 CYS378 SG2970 3.300 3.606 2.788 3.050 1.970 2.271 1.998 CYS384 SG3017 3.122 3.499 2.664 2.862 1.779 2.088 1.827 HIS386 NE23036 2.958 3.195 2.565 2.598 1.765 2.188 1.590 MET394 SD3115 3.569 4.001 1.309 2.309 2.583 2.394 1.131 CYS450 SG3564 4.794 4.856 2.361 3.623 3.769 3.623 2.482 CYS462 SG3645 4.954 5.052 2.384 3.762 3.901 3.703 2.607 HIS491 NE23860 3.938 4.036 1.953 2.750 3.053 3.044 1.699 HIS331 MET339 CYS378 CYS384 HIS386 MET394 CYS450 NE22596 SD2662 SG2970 SG3017 NE23036 SD3115 SG3564 MET339 SD2662 2.198 CYS378 SG2970 3.007 1.364 CYS384 SG3017 2.860 1.162 0.202 HIS386 NE23036 2.587 1.119 0.563 0.470 MET394 SD3115 1.364 1.855 1.999 1.918 1.664 CYS450 SG3564 2.558 2.995 2.514 2.545 2.340 1.371 CYS462 SG3645 2.655 3.121 2.629 2.663 2.483 1.486 0.202 HIS491 NE23860 1.824 2.332 2.180 2.149 1.829 0.710 0.917 CYS462 SG3645 HIS491 NE23860 1.091 Linking CYS-28 SG-226 and CYS-86 SG-699... Linking CYS-70 SG-568 and CYS-115 SG-895... Linking CYS-141 SG-1096 and CYS-160 SG-1242... Linking CYS-378 SG-2970 and CYS-384 SG-3017... Linking CYS-450 SG-3564 and CYS-462 SG-3645... Start terminus TYR-2: NH3+ End terminus LEU-496: COO- Checking for duplicate atoms.... Now there are 495 residues with 5087 atoms Making bonds... Number of bonds was 5207, now 5202 Generating angles, dihedrals and pairs... Before cleaning: 8104 pairs Before cleaning: 10145 dihedrals Making cmap torsions...There are 2623 dihedrals, 2788 impropers, 7653 angles 8104 pairs, 5202 bonds and 0 virtual sites Total mass 55217.920 a.m.u. Total charge -6.000 e Writing topology Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: amylase.pdb. The Gromos53a6 force field is used. --------- ETON ESAELP ------------ gcq#289: "Shaken, not Stirred" (J. Bond)
! pdb2gmx -f camelid.pdb -o camelid_h.pdb -p -ff gromos53a6 -ignh -water none
:-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description ------------------------------------------------------------ -f camelid.pdb Input Structure file: gro g96 pdb tpr etc. -o camelid_h.pdb Output Structure file: gro g96 pdb etc. -p topol.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Structure file: gro g96 pdb etc. Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -nice int 0 Set the nicelevel -chainsep enum id_or_ter Condition in PDB files when a new chain should be started (adding termini): id_or_ter, id_and_ter, ter, id or interactive -merge enum no Merge multiple chains into a single [moleculetype]: no, all or interactive -ff string gromos53a6 Force field, interactive by default. Use -h for information. -water enum none Water model to use: select, none, spc, spce, tip3p, tip4p or tip5p -[no]inter bool no Set the next 8 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool no Interactive termini selection, instead of charged (default) -[no]lys bool no Interactive lysine selection, instead of charged -[no]arg bool no Interactive arginine selection, instead of charged -[no]asp bool no Interactive aspartic acid selection, instead of charged -[no]glu bool no Interactive glutamic acid selection, instead of charged -[no]gln bool no Interactive glutamine selection, instead of neutral -[no]his bool no Interactive histidine selection, instead of checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -dist real 0.3 Maximum donor-acceptor distance for a H-bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on phenylalanine, tryptophane and tyrosine -[no]ignh bool yes Ignore hydrogen atoms that are in the coordinate file -[no]missing bool no Continue when atoms are missing, dangerous -[no]v bool no Be slightly more verbose in messages -posrefc real 1000 Force constant for position restraints -vsite enum none Convert atoms to virtual sites: none, hydrogens or aromatics -[no]heavyh bool no Make hydrogen atoms heavy -[no]deuterate bool no Change the mass of hydrogens to 2 amu -[no]chargegrp bool yes Use charge groups in the .rtp file -[no]cmap bool yes Use cmap torsions (if enabled in the .rtp file) -[no]renum bool no Renumber the residues consecutively in the output -[no]rtpres bool no Use .rtp entry names as residue names Using the Gromos53a6 force field in directory gromos53a6.ff Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading camelid.pdb... Read 903 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 111 residues with 903 atoms chain #res #atoms 1 'B' 123 903 All occupancies are one Opening force field file /usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp Atomtype 1 Reading residue database... (gromos53a6) Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 108 Sorting it all out... Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.1# Processing chain 1 'B' (903 atoms, 123 residues) Identified residue GLN1 as a starting terminus. Identified residue VAL111 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS22 MET34 CYS45 MET82 CYS92 SG143 SD215 SG306 SD588 SG693 MET34 SD215 0.667 CYS45 SG306 1.465 1.705 MET82 SD588 1.290 1.645 1.477 CYS92 SG693 0.204 0.644 1.283 1.231 CYS100 SG792 1.473 1.646 0.204 1.609 1.284 Linking CYS-22 SG-143 and CYS-92 SG-693... Linking CYS-45 SG-306 and CYS-100 SG-792... Start terminus GLN-1: NH3+ End terminus VAL-111: COO- Checking for duplicate atoms.... Now there are 123 residues with 1176 atoms Making bonds... Warning: Long Bond (201-203 = 0.338522 nm) Number of bonds was 1202, now 1197 Generating angles, dihedrals and pairs... Before cleaning: 1935 pairs Before cleaning: 2304 dihedrals Making cmap torsions...There are 628 dihedrals, 603 impropers, 1748 angles 1935 pairs, 1197 bonds and 0 virtual sites Total mass 12878.351 a.m.u. Total charge 2.000 e Writing topology Back Off! I just backed up posre.itp to ./#posre.itp.1# Writing coordinate file... --------- PLEASE NOTE ------------ You have successfully generated a topology from: camelid.pdb. The Gromos53a6 force field is used. --------- ETON ESAELP ------------ gcq#17: "I Calculate My Birthright" (P.J. Harvey)
Об утилите mark_sur:
%%bash
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/preps/golovin/progs/lib
export PATH=${PATH}:/home/preps/golovin/progs/bin
mark_sur
Usage: mark_sur in_pdb_file out_pdb_file Mark the surface residues of a PDB file
Эта утилита для каждого атома определяет ASA (accesible surface area = поверхность, доступная для растворителя), которая обычно определяется по методу Ли-Ричардса, "качением" молекулу воды радиусом 1.4 А по срезам структуры. Если атом имеет ASA больше 1 А, он отмечается утилитой mark_sur как поверхностный.
С помощью этой утилиты нужно провести препроцессинг файлов.
%%bash
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/preps/golovin/progs/lib
export PATH=${PATH}:/home/preps/golovin/progs/bin
mark_sur amylase_h.pdb amylase_m.pdb > amylase_mark.txt
mark_sur camelid_h.pdb camelid_m.pdb > camelid_mark.txt
%%bash
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/preps/golovin/progs/lib
export PATH=${PATH}:/home/preps/golovin/progs/bin
zdock
Usage: zdock [options] -R [receptor.pdb] -L [ligand.pdb] Standard PDB format files must be processed by mark_sur to add atom radius, charge and atom type. If you know that some atoms are not in the binding site, you can block them by changing their atom type (column 55-56) to 19. Available options: -o filename : set the output filename (default to zdock.out) -N int : set the number of output predictions, (default to 2000) -S int : set the seed for the randomization of the starting PDBs (default to no randomization) -D : set rotational sampling to be dense, used only if zdock output will be further processed by more detailed binding energy calculations (default to none) -F : fix the receptor, preventing its rotation and switching with ligand during execution.
Из файлов camelid_m.pdb и amylase_m.pdb были удалены строчки MODEL и TER. Теперь можно запускать zdock (15 предсказаний).
%%bash
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/preps/golovin/progs/lib
export PATH=${PATH}:/home/preps/golovin/progs/bin
zdock -N 15 -R camelid_m.pdb -L amylase_m.pdb
ZDOCK has successfully completed and zdock.out has been created.
Делаем копию файла zdock.out и в ней удаляем вторую строчку.
%%bash
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/preps/golovin/progs/lib
export PATH=${PATH}:/home/preps/golovin/progs/bin
zrank zdock.out.cp 1 10
sort -n -k2 zdock.out.cp.zr.out | head
6 -8.39476 10 0 12 0 5 0 7 0 8 0 13 1.38775 1 2.13888 2 39.7335 9 658.359
%%bash
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/preps/golovin/progs/lib
export PATH=${PATH}:/home/preps/golovin/progs/bin
ln -s /home/preps/golovin/progs/bin/create_lig
create.pl zdock.out