Fe3p Heme Iron Unrecognized Despite Loading Hem Params

[Anonymous]

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:

/usr/local/rosetta3.2.1/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/docking_protocol.default.linuxgccrelease
-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
IO_STRING HEM Z
TYPE LIGAND
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!

[Anonymous]

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.

[Anonymous]

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

[Anonymous]

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!
THANKS

[Anonymous]

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

[Anonymous]

That works!
Thank you so much Rocco.

[Anonymous]

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.)

[Author]

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