Using 2 non-standard residues in one run

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- March 9, 2011 at 5:24 am #818
  Anonymous
  How do I identify two ligand residue type files? I’m docking two proteins, each with a prosthetic group that’s near the docking interface. I’ve created the residue type files. I can only get it to recognize one of the two residues, whether I use -extra_res_fa [They’re both in the same dir], or whether I use two -extra_res_fa statements, or if I string the full path & file names of both files after the -extra_res_fa statement. A while back, someone explained to me that I can also put the .params files into rosetta_database/chemical/residue_type_sets/fa_standard/residue_types & add the appropriate lines to the file residue_types.txt. Well, I tried that. No go. When I went back to the -extra_res_fa flag, I got an error message that ‘residue type names must be unique’ or something close to it. So it’s sort of recognizing I put something in there, even if it refuses to use it. I renamed the edited residue_types.txt file & moved the original back in place, but I’m still stuck.
  
  Yes, I should probably upgrade to 3.2, but I REALLY need this to run. After that, I can think about it.
  
  Thanks!
- March 9, 2011 at 3:18 pm #5140
  Anonymous
  -extra_res_fa file1 file2 ought to work. I think your problem is “I got an error message that ‘residue type names must be unique'”.
  
  What are your residue names? You can just attach the params files if you wish.
- March 9, 2011 at 3:21 pm #5142
  Anonymous
  I think that your ligands are named the same in the params and protein file. The default residue name is LG1. Open your params file and rename the name and the IO_STRING line to a different name than LG1. Also, you need to edit your pdb file so that it corresponds to the changed name in your params file. Alternatively, you can run molfile_to_params.py with the flag -n letter name> to create the params file and pdb file with different names.
  
  I have attached a documentation file on the parameters file for your reference. This file was created for the purpose of the Rosetta Workshop. This article along with full tutorials on several applications will be made public next week on the Meiler Lab website.
- March 9, 2011 at 9:34 pm #5145
  Anonymous
  The bizarre thing is that in a Rosetta relax job I was doing about a month ago, I had two substrates for that protein & used the -extra_res_fa flag just like it’s used below & it was just fine…
  Here’s the command file: /opt/rosetta/rosetta_source/bin/docking_protocol.linuxgccdebug @flag3 > dockingHNbHEM.log
  Here’s flag3: -in -file -s cytHNbhems.pdb # the input file should have two single, complete chains A and B # for Ab molecules (with L+H chains) use -docking::partners flag below -path -database /opt/rosetta/rosetta_database/ # customize this to point to your installation directory -extra_res_fa /home/newhojs/Desktop/RosettaParams/HEC.params /home/newhojs/Desktop/RosettaParams/HEM.params -docking -dock_pert 45 10 # rotates partner1 (chain A) before docking proteins together #-randomize2 # rotates partner2 (chain before docking proteins together -partners AD_BE # defines docking partners by ChainID; see manual -out -nstruct 1000 # this should be set to a large number for effective sampling -mute core.util.prof # reduces copious output, without overdoing as with -mute all -file -o dockHNbHEM # scorefile will be named dock_output.sc (or .fasc for fullatom) -fullatom # fullatom is commented out for fast low-res "centroid mode" run
  
  Here’s the error message: ERROR: switch_to_residue_type_set fails
  ERROR:: Exit from: src/core/chemical/util.cc line: 573 docking_protocol.linuxgccdebug: src/utility/exit.cc:119: void utility::exit(const std::string&, int, const std::string&, int): Assertion `false' failed. ./command3: line 1: 9961 Aborted /opt/rosetta/rosetta_source/bin/docking_protocol.linuxgccdebug @flag3 > dockingHNbHEM.log
  
  Here’s the params files: IO_STRING HEC Z TYPE LIGAND AA UNK ATOM FE1 Fe3p X 3.03 ATOM N1 Npro X -0.34 ATOM C5 aroC X -0.08 ATOM C1 aroC X -0.08 ATOM C30 CH1 X -0.06 ATOM N4 Nhis X -0.50 ATOM C27 aroC X -0.08 ATOM C4 aroC X -0.08 ATOM C23 aroC X -0.08 ATOM N3 Npro X -0.34 ATOM C20 aroC X -0.08 ATOM C3 aroC X -0.08 ATOM C16 aroC X -0.08 ATOM N2 Nhis X -0.50 ATOM C13 CH1 X -0.06 ATOM C2 aroC X -0.08 ATOM C8 aroC X -0.08 ATOM C7 aroC X -0.08 ATOM C6 aroC X -0.08 ATOM C10 CH2 X -0.15 ATOM C11 CH2 X -0.15 ATOM C12 COO X 0.65 ATOM O1 OOC X -0.73 ATOM O2 OOC X -0.73 ATOM H10 Hapo X 0.13 ATOM H11 Hapo X 0.13 ATOM H8 Hapo X 0.13 ATOM H9 Hapo X 0.13 ATOM C9 CH3 X -0.24 ATOM H5 Hapo X 0.13 ATOM H6 Hapo X 0.13 ATOM H7 Hapo X 0.13 ATOM H2 Haro X 0.15 ATOM C14 aroC X -0.08 ATOM C15 aroC X -0.08 ATOM C18 aroC X -0.08 ATOM C19 aroC X -0.08 ATOM H15 Haro X 0.15 ATOM H16 Haro X 0.15 ATOM C17 CH3 X -0.24 ATOM H12 Hapo X 0.13 ATOM H13 Hapo X 0.13 ATOM H14 Hapo X 0.13 ATOM H3 Haro X 0.15 ATOM C21 aroC X -0.08 ATOM C22 aroC X -0.08 ATOM C25 aroC X -0.08 ATOM C26 aroC X -0.08 ATOM H20 Haro X 0.15 ATOM H21 Haro X 0.15 ATOM C24 CH3 X -0.24 ATOM H17 Hapo X 0.13 ATOM H18 Hapo X 0.13 ATOM H19 Hapo X 0.13 ATOM H4 Haro X 0.15 ATOM C28 aroC X -0.08 ATOM C29 aroC X -0.08 ATOM C32 CH2 X -0.15 ATOM C33 CH2 X -0.15 ATOM C34 COO X 0.65 ATOM O3 OOC X -0.73 ATOM O4 OOC X -0.73 ATOM H27 Hapo X 0.13 ATOM H28 Hapo X 0.13 ATOM H25 Hapo X 0.13 ATOM H26 Hapo X 0.13 ATOM C31 CH3 X -0.24 ATOM H22 Hapo X 0.13 ATOM H23 Hapo X 0.13 ATOM H24 Hapo X 0.13 ATOM H1 Haro X 0.15 BOND FE1 N1 BOND FE1 N2 BOND FE1 N3 BOND FE1 N4 BOND C1 C5 BOND C1 C30 BOND C1 H1 BOND C2 C8 BOND C2 C13 BOND C2 H2 BOND C3 C16 BOND C3 C20 BOND C3 H3 BOND C4 C23 BOND C4 C27 BOND C4 H4 BOND N1 C5 BOND N1 C8 BOND C5 C6 BOND C6 C7 BOND C6 C10 BOND C7 C8 BOND C7 C9 BOND C9 H5 BOND C9 H6 BOND C9 H7 BOND C10 C11 BOND C10 H8 BOND C10 H9 BOND C11 C12 BOND C11 H10 BOND C11 H11 BOND C12 O1 BOND C12 O2 BOND N2 C13 BOND N2 C16 BOND C13 C14 BOND C14 C15 BOND C14 C17 BOND C15 C16 BOND C15 C18 BOND C17 H12 BOND C17 H13 BOND C17 H14 BOND C18 C19 BOND C19 H15 BOND C19 H16 BOND N3 C20 BOND N3 C23 BOND C20 C21 BOND C21 C22 BOND C21 C24 BOND C22 C23 BOND C22 C25 BOND C24 H17 BOND C24 H18 BOND C24 H19 BOND C25 C26 BOND C26 H20 BOND C26 H21 BOND N4 C27 BOND N4 C30 BOND C27 C28 BOND C28 C29 BOND C28 C31 BOND C29 C30 BOND C29 C32 BOND C31 H22 BOND C31 H23 BOND C31 H24 BOND C32 C33 BOND C32 H25 BOND C32 H26 BOND C33 C34 BOND C33 H27 BOND C33 H28 BOND C34 O3 BOND C34 O4 CHI 1 C7 C6 C10 C11 CHI 2 C6 C10 C11 C12 CHI 3 C10 C11 C12 O1 CHI 4 C14 C15 C18 C19 CHI 5 C21 C22 C25 C26 CHI 6 C28 C29 C32 C33 CHI 7 C29 C32 C33 C34 CHI 8 C32 C33 C34 O3 NBR_ATOM FE1 NBR_RADIUS 10.143759 ICOOR_INTERNAL FE1 0.000000 0.000000 ICOOR_INTERNAL N1 0.000000 180.000000 ICOOR_INTERNAL C5 0.000000 54.660379 ICOOR_INTERNAL C1 -6.586011 54.336681 ICOOR_INTERNAL C30 -1.310092 53.026685 ICOOR_INTERNAL N4 3.178322 55.412187 ICOOR_INTERNAL C27 179.766114 72.404581 ICOOR_INTERNAL C4 -176.689499 54.336456 ICOOR_INTERNAL C23 4.664931 54.848053 ICOOR_INTERNAL N3 -1.669728 53.668239 ICOOR_INTERNAL C20 177.059072 71.957833 ICOOR_INTERNAL C3 170.758199 53.234986 ICOOR_INTERNAL C16 -1.462604 54.270064 ICOOR_INTERNAL N2 3.883042 54.384569 ICOOR_INTERNAL C13 -178.983767 71.628173 ICOOR_INTERNAL C2 -172.138519 54.360913 ICOOR_INTERNAL C8 -1.129188 53.920239 ICOOR_INTERNAL C7 174.605224 54.849541 ICOOR_INTERNAL C6 -177.898759 73.243228 ICOOR_INTERNAL C10 -177.559930 53.729009 ICOOR_INTERNAL C11 85.198696 71.021463 ICOOR_INTERNAL C12 -173.456319 64.867780 ICOOR_INTERNAL O1 -171.979796 61.079225 ICOOR_INTERNAL O2 158.403086 61.882856 ICOOR_INTERNAL H10 120.032069 70.515699 ICOOR_INTERNAL H11 119.956885 70.480445 ICOOR_INTERNAL H8 119.996735 70.471162 ICOOR_INTERNAL H9 120.008746 70.494171 ICOOR_INTERNAL C9 176.914383 54.004549 ICOOR_INTERNAL H5 3.723533 70.477804 ICOOR_INTERNAL H6 119.978765 70.476813 ICOOR_INTERNAL H7 120.008948 70.488720 ICOOR_INTERNAL H2 179.973424 66.079337 ICOOR_INTERNAL C14 179.283045 71.330991 ICOOR_INTERNAL C15 -7.996483 73.241231 ICOOR_INTERNAL C18 -174.144022 51.604030 ICOOR_INTERNAL C19 66.249405 67.869197 ICOOR_INTERNAL H15 52.501275 60.032524 ICOOR_INTERNAL H16 179.977649 60.007713 ICOOR_INTERNAL C17 -179.182966 54.170936 ICOOR_INTERNAL H12 179.991487 70.516233 ICOOR_INTERNAL H13 119.993531 70.506494 ICOOR_INTERNAL H14 120.009324 70.505436 ICOOR_INTERNAL H3 179.985731 65.716502 ICOOR_INTERNAL C21 -174.153583 70.710377 ICOOR_INTERNAL C22 8.315345 73.010494 ICOOR_INTERNAL C25 166.716274 53.501856 ICOOR_INTERNAL C26 59.214106 65.318506 ICOOR_INTERNAL H20 54.464796 60.016730 ICOOR_INTERNAL H21 -179.993054 59.968409 ICOOR_INTERNAL C24 172.117769 54.968887 ICOOR_INTERNAL H17 179.998258 70.524320 ICOOR_INTERNAL H18 120.016568 70.516338 ICOOR_INTERNAL H19 119.957354 70.491266 ICOOR_INTERNAL H4 179.989447 65.160852 ICOOR_INTERNAL C28 176.886626 70.605744 ICOOR_INTERNAL C29 -1.547204 73.299845 ICOOR_INTERNAL C32 -172.881452 53.916497 ICOOR_INTERNAL C33 99.249070 71.805494 ICOOR_INTERNAL C34 -166.444495 63.796088 ICOOR_INTERNAL O3 -14.435926 56.186929 ICOOR_INTERNAL O4 -176.639275 63.168415 ICOOR_INTERNAL H27 119.990087 70.473804 ICOOR_INTERNAL H28 120.014449 70.497209 ICOOR_INTERNAL H25 120.024250 70.520827 ICOOR_INTERNAL H26 119.989436 70.497255 ICOOR_INTERNAL C31 -176.288965 54.817664 ICOOR_INTERNAL H22 -179.973158 70.482133 ICOOR_INTERNAL H23 119.984968 70.517008 ICOOR_INTERNAL H24 119.966328 70.495184 ICOOR_INTERNAL H1 -179.977731 59.974848NAME HEC 0.000000 FE1 N1 C5 2.012319 FE1 N1 C5 1.354809 N1 FE1 C5 1.388351 C5 N1 FE1 1.382496 C1 C5 N1 1.351924 C30 C1 C5 1.391242 N4 C30 C1 1.380845 C27 N4 C30 1.388149 C4 C27 N4 1.369640 C23 C4 C27 1.363982 N3 C23 C4 1.381039 C20 N3 C23 1.376272 C3 C20 N3 1.357843 C16 C3 C20 1.358180 N2 C16 C3 1.389261 C13 N2 C16 1.384769 C2 C13 N2 1.401763 C8 C2 C13 1.398926 C7 C8 C2 1.519287 C6 C7 C8 1.517462 C10 C6 C7 1.524211 C11 C10 C6 1.237515 C12 C11 C10 1.297187 C12 C11 O1 1.090123 C11 C10 C12 1.090030 C11 C10 H10 1.089967 C10 C6 C11 1.089979 C10 C6 H8 1.522841 C7 C8 C6 1.089658 C9 C7 C8 1.090041 C9 C7 H5 1.090153 C9 C7 H6 1.080212 C2 C13 C8 1.396356 C13 N2 C2 1.409135 C14 C13 N2 1.530470 C15 C14 C13 1.525260 C18 C15 C14 1.079934 C19 C18 C15 1.080212 C19 C18 H15 1.522483 C14 C13 C15 1.090688 C17 C14 C13 1.089482 C17 C14 H12 1.089913 C17 C14 H13 1.080003 C3 C20 C16 1.380147 C20 N3 C3 1.388951 C21 C20 N3 1.523677 C22 C21 C20 1.519330 C25 C22 C21 1.080001 C26 C25 C22 1.079877 C26 C25 H20 1.513098 C21 C20 C22 1.090028 C24 C21 C20 1.089789 C24 C21 H17 1.090404 C24 C21 H18 1.080262 C4 C27 C23 1.401498 C27 N4 C4 1.395281 C28 C27 N4 1.525714 C29 C28 C27 1.528258 C32 C29 C28 1.539529 C33 C32 C29 1.229820 C34 C33 C32 1.299301 C34 C33 O3 1.089676 C33 C32 C34 1.090109 C33 C32 H27 1.089913 C32 C29 C33 1.090408 C32 C29 H25 1.522964 C28 C27 C29 1.089832 C31 C28 C27 1.089850 C31 C28 H22 1.089856 C31 C28 H23 1.080253 C1 C5 C30
  I do know about LG1 --> something else:-)
  & here's HEM.params: NAME HEM IO_STRING HEM Z TYPE LIGAND AA UNK ATOM FE1 Fe3p X 3.02 ATOM N1 Npro X -0.35 ATOM C5 aroC X -0.09 ATOM C1 aroC X -0.09 ATOM C30 aroC X -0.09 ATOM N4 Npro X -0.35 ATOM C27 aroC X -0.09 ATOM C4 aroC X -0.09 ATOM C23 aroC X -0.09 ATOM N3 Npro X -0.35 ATOM C20 aroC X -0.09 ATOM C3 aroC X -0.09 ATOM C16 aroC X -0.09 ATOM N2 Npro X -0.35 ATOM C13 aroC X -0.09 ATOM C2 aroC X -0.09 ATOM C8 aroC X -0.09 ATOM C7 aroC X -0.09 ATOM C6 aroC X -0.09 ATOM C10 CH2 X -0.16 ATOM C11 CH2 X -0.16 ATOM C12 COO X 0.64 ATOM O1 OOC X -0.74 ATOM O2 OOC X -0.74 ATOM H10 Hapo X 0.12 ATOM H11 Hapo X 0.12 ATOM H8 Hapo X 0.12 ATOM H9 Hapo X 0.12 ATOM C9 CH3 X -0.25 ATOM H5 Hapo X 0.12 ATOM H6 Hapo X 0.12 ATOM H7 Hapo X 0.12 ATOM H2 Haro X 0.14 ATOM C14 aroC X -0.09 ATOM C15 aroC X -0.09 ATOM C18 aroC X -0.09 ATOM C19 aroC X -0.09 ATOM H16 Haro X 0.14 ATOM H17 Haro X 0.14 ATOM H15 Haro X 0.14 ATOM C17 CH3 X -0.25 ATOM H12 Hapo X 0.12 ATOM H13 Hapo X 0.12 ATOM H14 Hapo X 0.12 ATOM H3 Haro X 0.14 ATOM C21 aroC X -0.09 ATOM C22 aroC X -0.09 ATOM C25 aroC X -0.09 ATOM C26 aroC X -0.09 ATOM H22 Haro X 0.14 ATOM H23 Haro X 0.14 ATOM H21 Haro X 0.14 ATOM C24 CH3 X -0.25 ATOM H18 Hapo X 0.12 ATOM H19 Hapo X 0.12 ATOM H20 Hapo X 0.12 ATOM H4 Haro X 0.14 ATOM C28 aroC X -0.09 ATOM C29 aroC X -0.09 ATOM C32 CH2 X -0.16 ATOM C33 CH2 X -0.16 ATOM C34 COO X 0.64 ATOM O3 OOC X -0.74 ATOM O4 OOC X -0.74 ATOM H29 Hapo X 0.12 ATOM H30 Hapo X 0.12 ATOM H27 Hapo X 0.12 ATOM H28 Hapo X 0.12 ATOM C31 CH3 X -0.25 ATOM H24 Hapo X 0.12 ATOM H25 Hapo X 0.12 ATOM H26 Hapo X 0.12 ATOM H1 Haro X 0.14 BOND FE1 N1 BOND FE1 N2 BOND FE1 N3 BOND FE1 N4 BOND C1 C5 BOND C1 C30 BOND C1 H1 BOND C2 C8 BOND C2 C13 BOND C2 H2 BOND C3 C16 BOND C3 C20 BOND C3 H3 BOND C4 C23 BOND C4 C27 BOND C4 H4 BOND N1 C5 BOND N1 C8 BOND C5 C6 BOND C6 C7 BOND C6 C10 BOND C7 C8 BOND C7 C9 BOND C9 H5 BOND C9 H6 BOND C9 H7 BOND C10 C11 BOND C10 H8 BOND C10 H9 BOND C11 C12 BOND C11 H10 BOND C11 H11 BOND C12 O1 BOND C12 O2 BOND N2 C13 BOND N2 C16 BOND C13 C14 BOND C14 C15 BOND C14 C17 BOND C15 C16 BOND C15 C18 BOND C17 H12 BOND C17 H13 BOND C17 H14 BOND C18 C19 BOND C18 H15 BOND C19 H16 BOND C19 H17 BOND N3 C20 BOND N3 C23 BOND C20 C21 BOND C21 C22 BOND C21 C24 BOND C22 C23 BOND C22 C25 BOND C24 H18 BOND C24 H19 BOND C24 H20 BOND C25 C26 BOND C25 H21 BOND C26 H22 BOND C26 H23 BOND N4 C27 BOND N4 C30 BOND C27 C28 BOND C28 C29 BOND C28 C31 BOND C29 C30 BOND C29 C32 BOND C31 H24 BOND C31 H25 BOND C31 H26 BOND C32 C33 BOND C32 H27 BOND C32 H28 BOND C33 C34 BOND C33 H29 BOND C33 H30 BOND C34 O3 BOND C34 O4 CHI 1 C7 C6 C10 C11 CHI 2 C6 C10 C11 C12 CHI 3 C10 C11 C12 O1 CHI 4 C14 C15 C18 C19 CHI 5 C21 C22 C25 C26 CHI 6 C28 C29 C32 C33 CHI 7 C29 C32 C33 C34 CHI 8 C32 C33 C34 O3 NBR_ATOM FE1 NBR_RADIUS 10.164055 ICOOR_INTERNAL FE1 0.000000 0.000000 0.000000 FE1 N1 C5 ICOOR_INTERNAL N1 0.000000 180.000000 2.056121 FE1 N1 C5 ICOOR_INTERNAL C5 0.000001 55.656149 1.379181 N1 FE1 C5 ICOOR_INTERNAL C1 -5.492646 53.509860 1.370981 C5 N1 FE1 ICOOR_INTERNAL C30 8.356377 53.798025 1.360837 C1 C5 N1 ICOOR_INTERNAL N4 -2.263845 54.885368 1.383394 C30 C1 C5 ICOOR_INTERNAL C27 179.599537 69.440490 1.389028 N4 C30 C1 ICOOR_INTERNAL C4 178.683971 54.296236 1.360500 C27 N4 C30 ICOOR_INTERNAL C23 -7.889195 53.083678 1.373162 C4 C27 N4 ICOOR_INTERNAL N3 11.037674 53.069173 1.367622 C23 C4 C27 ICOOR_INTERNAL C20 178.114015 72.023208 1.381755 N3 C23 C4 ICOOR_INTERNAL C3 178.822909 54.308175 1.369602 C20 N3 C23 ICOOR_INTERNAL C16 -1.072649 55.456142 1.375001 C3 C20 N3 ICOOR_INTERNAL N2 -0.174987 53.589380 1.378055 C16 C3 C20 ICOOR_INTERNAL C13 179.066136 73.501726 1.392129 N2 C16 C3 ICOOR_INTERNAL C2 179.082664 54.306785 1.365300 C13 N2 C16 ICOOR_INTERNAL C8 -2.712310 54.922021 1.369593 C2 C13 N2 ICOOR_INTERNAL C7 178.365707 54.692869 1.443864 C8 C2 C13 ICOOR_INTERNAL C6 -179.129950 72.139671 1.327011 C7 C8 C2 ICOOR_INTERNAL C10 -179.922216 53.430587 1.550825 C6 C7 C8 ICOOR_INTERNAL C11 -79.484575 68.928471 1.536701 C10 C6 C7 ICOOR_INTERNAL C12 -72.925223 68.400658 1.517559 C11 C10 C6 ICOOR_INTERNAL O1 -45.585859 60.378301 1.260016 C12 C11 C10 ICOOR_INTERNAL O2 -179.675497 61.826676 1.254407 C12 C11 O1 ICOOR_INTERNAL H10 119.973220 70.478249 1.089828 C11 C10 C12 ICOOR_INTERNAL H11 120.034615 70.494219 1.090017 C11 C10 H10 ICOOR_INTERNAL H8 119.991969 70.514884 1.089565 C10 C6 C11 ICOOR_INTERNAL H9 120.005251 70.514645 1.089744 C10 C6 H8 ICOOR_INTERNAL C9 179.146059 54.336754 1.558623 C7 C8 C6 ICOOR_INTERNAL H5 1.025538 70.532152 1.089595 C9 C7 C8 ICOOR_INTERNAL H6 120.006273 70.499727 1.089729 C9 C7 H5 ICOOR_INTERNAL H7 119.988978 70.498127 1.089941 C9 C7 H6 ICOOR_INTERNAL H2 -179.993145 65.077769 1.080608 C2 C13 C8 ICOOR_INTERNAL C14 -179.283654 71.204455 1.440889 C13 N2 C2 ICOOR_INTERNAL C15 0.140921 72.602019 1.331736 C14 C13 N2 ICOOR_INTERNAL C18 -179.657583 52.631448 1.537050 C15 C14 C13 ICOOR_INTERNAL C19 -92.127357 60.588091 1.330616 C18 C15 C14 ICOOR_INTERNAL H16 -179.994511 60.004845 1.079831 C19 C18 C15 ICOOR_INTERNAL H17 179.967439 60.023557 1.079617 C19 C18 H16 ICOOR_INTERNAL H15 179.985928 60.013849 1.079772 C18 C15 C19 ICOOR_INTERNAL C17 -179.905285 54.452076 1.546264 C14 C13 C15 ICOOR_INTERNAL H12 -179.973708 70.492831 1.090364 C17 C14 C13 ICOOR_INTERNAL H13 119.991468 70.484395 1.089889 C17 C14 H12 ICOOR_INTERNAL H14 119.972526 70.498735 1.090346 C17 C14 H13 ICOOR_INTERNAL H3 -179.982279 64.548895 1.080576 C3 C20 C16 ICOOR_INTERNAL C21 -179.599849 71.870868 1.443831 C20 N3 C3 ICOOR_INTERNAL C22 0.880762 72.589705 1.340662 C21 C20 N3 ICOOR_INTERNAL C25 179.846622 52.184238 1.538343 C22 C21 C20 ICOOR_INTERNAL C26 -25.550894 58.571131 1.332881 C25 C22 C21 ICOOR_INTERNAL H22 -179.977574 59.981943 1.079606 C26 C25 C22 ICOOR_INTERNAL H23 179.956444 59.985101 1.079706 C26 C25 H22 ICOOR_INTERNAL H21 179.973896 59.992672 1.080542 C25 C22 C26 ICOOR_INTERNAL C24 178.032179 54.437287 1.545322 C21 C20 C22 ICOOR_INTERNAL H18 179.997220 70.494092 1.090478 C24 C21 C20 ICOOR_INTERNAL H19 119.998033 70.472764 1.090470 C24 C21 H18 ICOOR_INTERNAL H20 119.969628 70.499860 1.090105 C24 C21 H19 ICOOR_INTERNAL H4 -179.992594 66.905651 1.080453 C4 C27 C23 ICOOR_INTERNAL C28 -179.169896 70.998142 1.433080 C27 N4 C4 ICOOR_INTERNAL C29 0.205119 74.269098 1.496605 C28 C27 N4 ICOOR_INTERNAL C32 178.305126 54.117620 1.542623 C29 C28 C27 ICOOR_INTERNAL C33 -95.260538 73.364588 1.528215 C32 C29 C28 ICOOR_INTERNAL C34 179.493163 71.192610 1.510376 C33 C32 C29 ICOOR_INTERNAL O3 -116.349051 61.634248 1.252864 C34 C33 C32 ICOOR_INTERNAL O4 179.084081 61.530409 1.246769 C34 C33 O3 ICOOR_INTERNAL H29 119.999737 70.477265 1.089919 C33 C32 C34 ICOOR_INTERNAL H30 119.980799 70.494883 1.089558 C33 C32 H29 ICOOR_INTERNAL H27 119.977786 70.465540 1.089907 C32 C29 C33 ICOOR_INTERNAL H28 120.005718 70.500995 1.089811 C32 C29 H27 ICOOR_INTERNAL C31 178.873221 52.103694 1.548324 C28 C27 C29 ICOOR_INTERNAL H24 -179.992315 70.518979 1.089824 C31 C28 C27 ICOOR_INTERNAL H25 119.997115 70.507384 1.090324 C31 C28 H24 ICOOR_INTERNAL H26 119.990354 70.498744 1.089612 C31 C28 H25 ICOOR_INTERNAL H1 -179.985189 60.007203 1.080523 C1 C5 C30
- March 10, 2011 at 5:00 pm #5154
  Anonymous
  If you look at the log file, there should be a line at the very end which reads “can not find a residue type that matches the residue (residue name) at position (position)” which should help debug things. If you can’t see it, that’s because stdout is buffered when redirected, and the line was left in the buffer (and not put to disk) when the program existed. Try re-running it with the output going to the screen, and you should see the line.
  
  That might not be necessary, though, as my guess from looking at the code near the error is that the docking protocol is trying to go (temporarily) from full atom mode to centroid mode for one step of the protocol, and it’s not finding the centroid-mode params file for the new residues. molfile_to_params should be able to generate the centroid mode params file (I forget the exact flag – do a “molfile_to_params.py -h” for the help), and then include them in the flags file with the -extra_res_cen flag (works like -extra_res_fa, but for centroid parameters, rather than full atom).
- March 10, 2011 at 7:51 pm #5157
  Anonymous
  That did do the trick! Thanks ever so much! For the convenience of future newbies reviewing this thread, the molfile_to_params flag is -c.
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