Fe3p Heme Iron Unrecognized Despite Loading Hem Params

Member Site Forums Rosetta 3 Rosetta 3 – General Fe3p Heme Iron Unrecognized Despite Loading Hem Params

Viewing 5 reply threads
  • Author
    • #1019

        Hi All,
        I am new to computational biology in general, so bear with me if this question is rudimentary. I am trying to dock two heme proteins together. We have trouble-shot other issues but we can’t seem to get this one. Here is what we do:

        -database /usr/local/rosetta3.2.1/rosetta_database
        -extra_res_cen /usr/local/rosetta3.2.1/rosetta_database/chemical/residue_type_sets/fa_standard/residue_types/heme/HEM.params
        -extra_res_fa /usr/local/rosetta3.2.1/rosetta_database/chemical/residue_type_sets/fa_standard/residue_types/heme/HEM.params
        -s protein.pdb

        NOTE: In the pdb, there is a TER card at the end of each protein and again at the end of each HEM. Both HEMs are named the same.

        This is the error we get:
        ERROR: unrecognized atom_type_name Fe3p
        ERROR:: Exit from: src/core/chemical/AtomTypeSet.hh line: 82

        When we removed one HEM group, leaving one, we got the same message. When we removed both HEM groups and did not have the flags -extra_res, the program ran fine.

        We think there is something wrong with our HEM.params file. But we don’t know what. So, I have also copied and pasted it below:

        NAME HEM
        AA UNK
        ATOM FE Fe3p X 3.03
        ATOM NC Npro X -0.34
        ATOM C4C aroC X -0.09
        ATOM C3C aroC X -0.09
        ATOM CAC CH1 X -0.06
        ATOM CBC CH2 X -0.15
        ATOM 1HBC Hapo X 0.12
        ATOM 2HBC Hapo X 0.12
        ATOM HAC Hapo X 0.12
        ATOM C2C aroC X -0.09
        ATOM CMC CH3 X -0.24
        ATOM 3HMC Hapo X 0.12
        ATOM 2HMC Hapo X 0.12
        ATOM 1HMC Hapo X 0.12
        ATOM C1C aroC X -0.09
        ATOM CHC aroC X -0.09
        ATOM C4B aroC X -0.09
        ATOM NB Npro X -0.34
        ATOM C1B aroC X -0.09
        ATOM C2B aroC X -0.09
        ATOM C3B aroC X -0.09
        ATOM CAB aroC X -0.09
        ATOM CBB aroC X -0.09
        ATOM 1HBB Haro X 0.14
        ATOM 2HBB Haro X 0.14
        ATOM HAB Haro X 0.14
        ATOM CMB CH3 X -0.24
        ATOM 2HMB Hapo X 0.12
        ATOM 3HMB Hapo X 0.12
        ATOM 1HMB Hapo X 0.12
        ATOM CHB aroC X -0.09
        ATOM C4A aroC X -0.09
        ATOM NA Npro X -0.34
        ATOM C1A aroC X -0.09
        ATOM CHA aroC X -0.09
        ATOM C4D aroC X -0.09
        ATOM C3D aroC X -0.09
        ATOM C2D aroC X -0.09
        ATOM CMD CH3 X -0.24
        ATOM 1HMD Hapo X 0.12
        ATOM 3HMD Hapo X 0.12
        ATOM 2HMD Hapo X 0.12
        ATOM C1D aroC X -0.09
        ATOM CHD aroC X -0.09
        ATOM HHD Haro X 0.14
        ATOM ND Npro X -0.34
        ATOM CAD CH2 X -0.15
        ATOM CBD CH2 X -0.15
        ATOM CGD COO X 0.65
        ATOM O1D OOC X -0.73
        ATOM O2D OOC X -0.73
        ATOM 1HBD Hapo X 0.12
        ATOM 2HBD Hapo X 0.12
        ATOM 2HAD Hapo X 0.12
        ATOM 1HAD Hapo X 0.12
        ATOM HHA Haro X 0.14
        ATOM C2A aroC X -0.09
        ATOM CAA CH2 X -0.15
        ATOM CBA CH2 X -0.15
        ATOM CGA COO X 0.65
        ATOM O2A OOC X -0.73
        ATOM O1A OOC X -0.73
        ATOM 1HBA Hapo X 0.12
        ATOM 2HBA Hapo X 0.12
        ATOM 1HAA Hapo X 0.12
        ATOM 2HAA Hapo X 0.12
        ATOM C3A aroC X -0.09
        ATOM CMA CH3 X -0.24
        ATOM 1HMA Hapo X 0.12
        ATOM 2HMA Hapo X 0.12
        ATOM 3HMA Hapo X 0.12
        ATOM HHB Haro X 0.14
        ATOM HHC Haro X 0.14
        BOND 1HBC CBC
        BOND CBC 2HBC
        BOND CBC CAC
        BOND HAC CAC
        BOND 1HMD CMD
        BOND 3HMD CMD
        BOND CAC C3C
        BOND CMD 2HMD
        BOND CMD C2D
        BOND HHD CHD
        BOND 3HMC CMC
        BOND C3C C4C
        BOND C3C C2C
        BOND CHD C4C
        BOND CHD C1D
        BOND C2D C1D
        BOND C2D C3D
        BOND 2HAD CAD
        BOND O1D CGD
        BOND C4C NC
        BOND CMC C2C
        BOND CMC 2HMC
        BOND CMC 1HMC
        BOND C2C C1C
        BOND C1D ND
        BOND 1HBD CBD
        BOND C3D CAD
        BOND C3D C4D
        BOND CAD CBD
        BOND CAD 1HAD
        BOND CGD CBD
        BOND CGD O2D
        BOND CBD 2HBD
        BOND NC C1C
        BOND NC FE
        BOND C1C CHC
        BOND ND C4D
        BOND ND FE
        BOND C4D CHA
        BOND HHC CHC
        BOND CHC C4B
        BOND FE NB
        BOND FE NA
        BOND CHA HHA
        BOND CHA C1A
        BOND C4B NB
        BOND C4B C3B
        BOND NB C1B
        BOND O2A CGA
        BOND C1A NA
        BOND C1A C2A
        BOND NA C4A
        BOND HAB CAB
        BOND 1HBA CBA
        BOND CGA O1A
        BOND CGA CBA
        BOND CAB C3B
        BOND CAB CBB
        BOND C3B C2B
        BOND C1B C2B
        BOND C1B CHB
        BOND CBA CAA
        BOND CBA 2HBA
        BOND C2A CAA
        BOND C2A C3A
        BOND 1HAA CAA
        BOND C4A CHB
        BOND C4A C3A
        BOND CBB 1HBB
        BOND CBB 2HBB
        BOND CAA 2HAA
        BOND C2B CMB
        BOND CHB HHB
        BOND C3A CMA
        BOND CMB 2HMB
        BOND CMB 3HMB
        BOND CMB 1HMB
        BOND CMA 1HMA
        BOND CMA 2HMA
        BOND CMA 3HMA
        CHI 1 C4C C3C CAC CBC
        CHI 2 C4D C3D CAD CBD
        CHI 3 C3D CAD CBD CGD
        CHI 4 CAD CBD CGD O1D
        CHI 5 CAA CBA CGA O2A
        CHI 6 C2B C3B CAB CBB
        CHI 7 C2A CAA CBA CGA
        CHI 8 C1A C2A CAA CBA
        NBR_ATOM FE
        NBR_RADIUS 10.102870
        ICOOR_INTERNAL FE 0.000000 0.000000 0.000000 FE NC C4C
        ICOOR_INTERNAL NC 0.000000 0.000000 2.019616 FE NC C4C
        ICOOR_INTERNAL C4C 0.000001 51.546905 1.378491 NC FE C4C
        ICOOR_INTERNAL C3C 167.350050 70.849878 1.449394 C4C NC FE
        ICOOR_INTERNAL CAC -177.460606 56.166742 1.543556 C3C C4C NC
        ICOOR_INTERNAL CBC -168.245243 54.823679 1.331846 CAC C3C C4C
        ICOOR_INTERNAL 1HBC 156.508210 63.988833 1.075696 CBC CAC C3C
        ICOOR_INTERNAL 2HBC -168.783134 35.430661 1.089554 CBC CAC 1HBC
        ICOOR_INTERNAL HAC 160.974134 61.458370 1.053918 CAC C3C CBC
        ICOOR_INTERNAL C2C 175.762311 72.344399 1.341451 C3C C4C CAC
        ICOOR_INTERNAL CMC -171.155589 50.285086 1.546352 C2C C3C C4C
        ICOOR_INTERNAL 3HMC -29.458798 63.187550 1.064514 CMC C2C C3C
        ICOOR_INTERNAL 2HMC 127.775051 62.498226 1.062195 CMC C2C 3HMC
        ICOOR_INTERNAL 1HMC 112.502558 72.862613 1.059472 CMC C2C 2HMC
        ICOOR_INTERNAL C1C 171.992367 72.446298 1.444712 C2C C3C CMC
        ICOOR_INTERNAL CHC -170.949647 54.606644 1.378958 C1C C2C C3C
        ICOOR_INTERNAL C4B 168.258384 49.070177 1.378724 CHC C1C C2C
        ICOOR_INTERNAL NB -4.317555 59.006416 1.379626 C4B CHC C1C
        ICOOR_INTERNAL C1B 179.104517 75.767026 1.388246 NB C4B CHC
        ICOOR_INTERNAL C2B 0.503670 69.590297 1.451915 C1B NB C4B
        ICOOR_INTERNAL C3B -0.160460 72.675629 1.337096 C2B C1B NB
        ICOOR_INTERNAL CAB -179.240274 50.179570 1.539032 C3B C2B C1B
        ICOOR_INTERNAL CBB -61.123349 53.252784 1.339602 CAB C3B C2B
        ICOOR_INTERNAL 1HBB 176.251170 48.645231 1.125351 CBB CAB C3B
        ICOOR_INTERNAL 2HBB -175.321978 60.760600 1.120508 CBB CAB 1HBB
        ICOOR_INTERNAL HAB -179.866974 46.372573 1.077683 CAB C3B CBB
        ICOOR_INTERNAL CMB 179.541826 55.834504 1.546665 C2B C1B C3B
        ICOOR_INTERNAL 2HMB 118.485896 65.981843 1.053873 CMB C2B C1B
        ICOOR_INTERNAL 3HMB 117.998032 53.914424 1.054970 CMB C2B 2HMB
        ICOOR_INTERNAL 1HMB 125.952522 60.704254 1.049142 CMB C2B 3HMB
        ICOOR_INTERNAL CHB 178.844778 55.579652 1.381934 C1B NB C2B
        ICOOR_INTERNAL C4A 6.687332 55.649317 1.376341 CHB C1B NB
        ICOOR_INTERNAL NA -7.391473 53.272072 1.385143 C4A CHB C1B
        ICOOR_INTERNAL C1A -179.664587 73.931753 1.390610 NA C4A CHB
        ICOOR_INTERNAL CHA 179.288570 57.969037 1.381084 C1A NA C4A
        ICOOR_INTERNAL C4D 4.137505 50.544172 1.375944 CHA C1A NA
        ICOOR_INTERNAL C3D -172.279106 52.716170 1.446393 C4D CHA C1A
        ICOOR_INTERNAL C2D -179.560348 71.280407 1.329584 C3D C4D CHA
        ICOOR_INTERNAL CMD 179.435117 50.585098 1.549575 C2D C3D C4D
        ICOOR_INTERNAL 1HMD -75.605959 68.859234 1.089693 CMD C2D C3D
        ICOOR_INTERNAL 3HMD -125.948864 76.927751 1.073727 CMD C2D 1HMD
        ICOOR_INTERNAL 2HMD -119.645644 71.050333 1.052134 CMD C2D 3HMD
        ICOOR_INTERNAL C1D 179.947709 72.962358 1.448892 C2D C3D CMD
        ICOOR_INTERNAL CHD -179.721516 55.410808 1.381838 C1D C2D C3D
        ICOOR_INTERNAL HHD -1.485443 63.354322 1.006133 CHD C1D C2D
        ICOOR_INTERNAL ND -179.904218 70.738640 1.384224 C1D C2D CHD
        ICOOR_INTERNAL CAD 179.444551 57.873905 1.544659 C3D C4D C2D
        ICOOR_INTERNAL CBD 91.938602 64.251588 1.531517 CAD C3D C4D
        ICOOR_INTERNAL CGD 179.031056 70.600458 1.511244 CBD CAD C3D
        ICOOR_INTERNAL O1D -83.258020 63.218869 1.264470 CGD CBD CAD
        ICOOR_INTERNAL O2D 178.789358 63.692904 1.259821 CGD CBD O1D
        ICOOR_INTERNAL 1HBD -138.753588 64.277483 1.077687 CBD CAD CGD
        ICOOR_INTERNAL 2HBD -88.069144 81.970263 1.066011 CBD CAD 1HBD
        ICOOR_INTERNAL 2HAD 122.272967 90.080231 1.078138 CAD C3D CBD
        ICOOR_INTERNAL 1HAD 132.856855 69.758539 1.067174 CAD C3D 2HAD
        ICOOR_INTERNAL HHA -175.042339 66.497320 1.061147 CHA C1A C4D
        ICOOR_INTERNAL C2A -179.313956 70.305850 1.453392 C1A NA CHA
        ICOOR_INTERNAL CAA -179.279918 53.161725 1.539686 C2A C1A NA
        ICOOR_INTERNAL CBA 75.974327 54.944842 1.514768 CAA C2A C1A
        ICOOR_INTERNAL CGA 8.978963 54.815172 1.502641 CBA CAA C2A
        ICOOR_INTERNAL O2A -24.609268 59.098050 1.256829 CGA CBA CAA
        ICOOR_INTERNAL O1A -179.987890 61.983996 1.256368 CGA CBA O2A
        ICOOR_INTERNAL 1HBA -121.538921 69.637565 0.996678 CBA CAA CGA
        ICOOR_INTERNAL 2HBA -137.707085 75.584836 1.011465 CBA CAA 1HBA
        ICOOR_INTERNAL 1HAA -124.943099 61.792068 1.071617 CAA C2A CBA
        ICOOR_INTERNAL 2HAA -96.815888 72.703223 1.060356 CAA C2A 1HAA
        ICOOR_INTERNAL C3A 179.236658 73.392962 1.332465 C2A C1A CAA
        ICOOR_INTERNAL CMA 179.876787 49.688866 1.548077 C3A C2A C1A
        ICOOR_INTERNAL 1HMA 144.807049 63.202155 1.039591 CMA C3A C2A
        ICOOR_INTERNAL 2HMA -123.336730 61.311555 1.060520 CMA C3A 1HMA
        ICOOR_INTERNAL 3HMA -114.924606 70.894895 1.069633 CMA C3A 2HMA
        ICOOR_INTERNAL HHB 171.998836 62.145666 1.014482 CHB C1B C4A
        ICOOR_INTERNAL HHC 175.273213 65.152337 1.010847 CHC C1C C4B

        Thanks in advance to anyone with advice!

      • #6013

          My guess is that you’re having issue because of the “-extra_res_cen /usr/local/rosetta3.2.1/rosetta_database/chemical/residue_type_sets/fa_standard/residue_types/heme/HEM.params” flag. There isn’t an Fe3p atom type in centroid mode, so Rosetta’s getting confused when you provide it with a full atom params file for use in centroid mode.

          Where did you get the heme parameters from? As far as I’m aware, they’re not part of the standard release database. If you generated them yourself, molfile_to_params.py has a -c option to also generate centroid version params files. If you got them from somewhere else, see if there was a centroid heme params file included with that distribution that you can use instead.

        • #6017

            We did, in fact, find the heme parameters in the rosetta database we downloaded. We did not generate them ourselves.
            Will try advice and update our progress. Thanks

          • #6018

              Thanks rmoretti,
              turns out the hem params we found were incorrect. We had found them by searching for HEM with the linux command find. Anyway, redoing the params with the command:
              python molfile_to_params.py -c HEM.mol2
              Gave us the fa and cen params that worked. Now we have our control system actually running!

            • #8973

                Hi all,

                I think I have got a similar problem but with sodium ion. I used centroid param file from chemical/residue_type_sets/centroid/residue_types/metal_ion and got the same message “ERROR: unrecognized atom_type_name Na1p”. I did not see any difference between sodium centroid and full atom param files in the database. molfile_to_params.py -c also doesn’t work for me as my mol2 file does not have dummy atoms.
                What would you recommend?
                Thanks in advance

              • #8978

                  That works!
                  Thank you so much Rocco.

                • #8975

                    Probably the best way to handle it is to copy the Na1p line from rosetta_database/chemical/atom_type_sets/fa_standard/atom_properties.txt to rosetta_database/chemical/atom_type_sets/centroid/atom_properties.txt

                    That should hopefully get Rosetta working with the sodium ions, though how accurately it will model the sodium interaction is unknown. (To be honest, how accurately Rosetta will model sodium in the full atom case is unknown, as I’m unaware of anyone doing benchmarking of protocols with sodium ions present.)

                Viewing 5 reply threads
                • You must be logged in to reply to this topic.