error for the pose reading:TRP:NtermProteinFull:triazolamerC missing: C1

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    • December 2, 2017 at 1:50 am #2797
      Anonymous

        Hi there,

        I have a pdb file from CHARMM format. When I use

        fixbb.default.linuxgccrelease -in:file:s step1_pdbreader.pdb -in:file:fullatom -resfile resfile_2 -ex1 -ex2 -extrachi_cutoff 1 -nstruct 50 >out

        I got this:

        core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it’s missing too many mainchain atoms:    1 A TRP TRP:NtermProteinFull:triazolamerC

        core.io.pose_from_sfr.PoseFromSFRBuilder: missing:  CT1

        and it skipped the first residue TRP.

        Here is the pdb part for the TRP residue:

        ATOM      1  N   TRP A   1       7.251   3.305  16.767  1.00  0.00      PROA

        ATOM      2  HT1 TRP A   1       6.843   4.234  16.538  1.00  0.00      PROA

        ATOM      3  HT2 TRP A   1       8.122   3.435  17.320  1.00  0.00      PROA

        ATOM      4  HT3 TRP A   1       6.567   2.754  17.324  1.00  0.00      PROA

        ATOM      5  CA  TRP A   1       7.557   2.599  15.546  1.00  0.00      PROA

        ATOM      6  HA  TRP A   1       8.267   3.191  14.989  1.00  0.00      PROA

        ATOM      7  CB  TRP A   1       8.166   1.159  15.879  1.00  0.00      PROA

        ATOM      8  HB1 TRP A   1       7.351   0.463  16.172  1.00  0.00      PROA

        ATOM      9  HB2 TRP A   1       8.893   1.241  16.715  1.00  0.00      PROA

        ATOM     10  CG  TRP A   1       8.890   0.605  14.616  1.00  0.00      PROA

        ATOM     11  CD1 TRP A   1      10.150   0.911  14.232  1.00  0.00      PROA

        ATOM     12  HD1 TRP A   1      10.842   1.529  14.785  1.00  0.00      PROA

        ATOM     13  NE1 TRP A   1      10.421   0.277  12.963  1.00  0.00      PROA

        ATOM     14  HE1 TRP A   1      11.225   0.392  12.421  1.00  0.00      PROA

        ATOM     15  CE2 TRP A   1       9.349  -0.513  12.658  1.00  0.00      PROA

        ATOM     16  CD2 TRP A   1       8.357  -0.331  13.731  1.00  0.00      PROA

        ATOM     17  CE3 TRP A   1       7.185  -1.120  13.728  1.00  0.00      PROA

        ATOM     18  HE3 TRP A   1       6.482  -1.094  14.547  1.00  0.00      PROA

        ATOM     19  CZ3 TRP A   1       6.948  -1.922  12.672  1.00  0.00      PROA

        ATOM     20  HZ3 TRP A   1       6.007  -2.449  12.618  1.00  0.00      PROA

        ATOM     21  CZ2 TRP A   1       9.129  -1.420  11.648  1.00  0.00      PROA

        ATOM     22  HZ2 TRP A   1       9.858  -1.628  10.879  1.00  0.00      PROA

        ATOM     23  CH2 TRP A   1       7.862  -2.093  11.661  1.00  0.00      PROA

        ATOM     24  HH2 TRP A   1       7.618  -2.758  10.846  1.00  0.00      PROA

        ATOM     25  C   TRP A   1       6.432   2.553  14.567  1.00  0.00      PROA

        ATOM     26  O   TRP A   1       6.641   2.853  13.415  1.00  0.00      PROA

        So how could I let Rosetta read or recognize the first residue TRP?

        Thanks

      • December 2, 2017 at 6:03 pm #13931
        Anonymous

          I’m guessing it’s the name of the terminal hydrogens.

          Rosetta has heuristics to figure out which sorts of modified amino acids it’s looking at based on the sort of atom names it sees. This is only a heuristics, so it isn’t 100% accurate. Specifically, if you have atoms present which don’t match the names Rosetta expects, Rosetta may choose a different residue type modification.

          That’s what’s likely happening here. CHARMM’s convention for the three terminal amine hydrogens (HT1/HT2/HT3) is different from the Rosetta convention (1H/2H/3H). As such, it’s not recognizing those atoms and trying to find a variant type (“triazolamerC”) which does contain some of those atoms (HT2, specifically).

          The fix is to either rename those atoms or to just delete those lines. (Rosetta will rebuild missing hydrogens when it reads in the file.)

          • December 4, 2017 at 6:04 am #13933
            Anonymous

              Thank you so much for your reply. I deleted all hydrogens of TRP and now it works.

              By the way, do you know where I can find the parameter files for Rosetta, for example: how it name the atom type or atom name for different atoms from residues?

            • December 16, 2017 at 8:19 pm #13960
              Anonymous

                The parameter files that Rosetta uses for the default-loaded amino acids can be found in the Rosetta database (Rosetta/main/database/chemical/residue_types/fa_standard/).  Things like triazolamerC are patches rather than fully-fledged residue types, though (they’re in the same place, though).

                 

                 

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