Unrecognized residue Glc

[Anonymous]

Hi everyone,

I would like to use surface_docking on a pdb containing carbohydrates.
I put as residue name “Glc” in my pdb and I added the flag:

extra_res_fa=/media/storage/a/software/rosetta_src_2015.02.57538_bundle/main/database/chemical/residue_type_sets/fa_standard/residue_types/carbohydrates/to4-beta-D-Glcp.params

However I get the following error:

ERROR: No match found for unrecognized residue at position 1
Looking for lower-terminal residue with 3-letter code: Glc
ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 1216

Does someone know how to fix the problem?

Thanks,
Camille

[Anonymous]

To enable carbohydrate functionality in Rosetta, one has to use the -include_sugars flag. Do not use the -extra_res_fa flag.

 

In addition, the .pdb file must include HETNAM records.

An example HETNAM record looks like this: HETNAM Glc X 1 ->4)-beta-D-Glcp

…where Glc is the 3-letter code, X is the chain id, 1 is the residue number, and ->4)-beta-D-Glcp is the unique ResidueType name.

 

That being said, understand that carbohydrates are not fully implemented yet. It’s a work in progress and nothing is fully calibrated and little is published yet. If you need more assistance or would like to collaborate, please contact me at JWLabonte@jhu.edu.

 

~Labonte

[Anonymous]

Unfortunately I put both in my pdb but rosetta gives the same error. Do you have another idea to make it work ?
Thanks for your help.

[Anonymous]

Thank you for your answer.
I have some troubles concerning the way to write HETNAM records.
For example two blocks :
HETATM 1 C1 Glc B 1 0.148 -0.342 0.449 1.00 0.00 M0 C
HETATM 2 C2 Glc B 1 -0.032 -1.499 -0.536 1.00 0.00 M0 C
HETATM 3 O2 Glc B 1 0.766 -2.559 -0.003 1.00 0.00 M0 O
HETATM 4 C3 Glc B 1 0.439 -1.116 -1.918 1.00 0.00 M0 C
HETATM 5 O3 Glc B 1 0.032 -2.127 -2.864 1.00 0.00 M0 O
HETATM 6 C4 Glc B 1 -0.082 0.244 -2.336 1.00 0.00 M0 C
HETATM 7 O4 Glc B 1 0.535 0.701 -3.554 1.00 0.00 M0 O
HETATM 8 C5 Glc B 1 0.055 1.296 -1.279 1.00 0.00 M0 C
HETATM 9 O5 Glc B 1 -0.528 0.807 -0.055 1.00 0.00 M0 O
HETATM 10 C6 Glc B 1 -0.662 2.599 -1.588 1.00 0.00 M0 C
HETATM 11 O6 Glc B 1 -0.001 3.284 -2.637 1.00 0.00 M0 O
HETATM 12 HO2 Glc B 1 0.581 -2.603 0.955 1.00 0.00 M0 H
HETATM 13 HO3 Glc B 1 0.593 -1.956 -3.651 1.00 0.00 M0 H
HETATM 14 HO4 Glc B 1 0.519 -0.030 -4.223 0.00 0.00 M0 H
HETATM 15 HO6 Glc B 1 -0.569 4.012 -2.958 1.00 0.00 M0 H
HETATM 16 H1 Glc B 1 1.093 -0.153 0.621 1.00 0.00 M0 H
HETATM 17 H2 Glc B 1 -0.972 -1.774 -0.567 1.00 0.00 M0 H
HETATM 18 H3 Glc B 1 1.420 -1.078 -1.910 1.00 0.00 M0 H
HETATM 19 H4 Glc B 1 -1.041 0.143 -2.517 1.00 0.00 M0 H
HETATM 20 H5 Glc B 1 1.004 1.484 -1.131 1.00 0.00 M0 H
HETATM 21 H61 Glc B 1 -1.576 2.411 -1.846 1.00 0.00 M0 H
HETATM 22 H62 Glc B 1 -0.676 3.155 -0.794 1.00 0.00 M0 H
HETATM 23 C1 Glc B 2 -0.148 0.342 5.639 1.00 0.00 M0 C
HETATM 24 C2 Glc B 2 0.032 1.499 4.654 1.00 0.00 M0 C
HETATM 25 O2 Glc B 2 -0.766 2.559 5.187 1.00 0.00 M0 O
HETATM 26 C3 Glc B 2 -0.439 1.116 3.272 1.00 0.00 M0 C
HETATM 27 O3 Glc B 2 -0.032 2.127 2.326 1.00 0.00 M0 O
HETATM 28 C4 Glc B 2 0.082 -0.244 2.855 1.00 0.00 M0 C
HETATM 29 O4 Glc B 2 -0.535 -0.701 1.636 1.00 0.00 M0 O
HETATM 30 C5 Glc B 2 -0.055 -1.296 3.911 1.00 0.00 M0 C
HETATM 31 O5 Glc B 2 0.528 -0.807 5.135 1.00 0.00 M0 O
HETATM 32 C6 Glc B 2 0.662 -2.599 3.602 1.00 0.00 M0 C
HETATM 33 O6 Glc B 2 0.001 -3.284 2.553 1.00 0.00 M0 O
HETATM 34 HO2 Glc B 2 -0.581 2.603 6.145 1.00 0.00 M0 H
HETATM 35 HO3 Glc B 2 -0.593 1.956 1.539 1.00 0.00 M0 H
HETATM 36 HO6 Glc B 2 0.569 -4.012 2.232 1.00 0.00 M0 H
HETATM 37 H1 Glc B 2 -1.093 0.153 5.811 1.00 0.00 M0 H
HETATM 38 H2 Glc B 2 0.972 1.774 4.623 1.00 0.00 M0 H
HETATM 39 H3 Glc B 2 -1.420 1.078 3.280 1.00 0.00 M0 H
HETATM 40 H4 Glc B 2 1.041 -0.143 2.673 1.00 0.00 M0 H
HETATM 41 H5 Glc B 2 -1.004 -1.484 4.059 1.00 0.00 M0 H
HETATM 42 H61 Glc B 2 1.576 -2.411 3.344 1.00 0.00 M0 H
HETATM 43 H62 Glc B 2 0.676 -3.155 4.396 1.00 0.00 M0 H

should be replaced by:
HETNAM Glc B 1 ->4)-beta-D-Glcp
HETNAM Glc B 2 ->4)-beta-D-Glcp
?

How can I define the coordinates then?

Thanks,
Camille

[Anonymous]

The HETNAM records are different from the HETATM record.

HETNAM records are additional records found in the “header” portion of the PDB (http://www.wwpdb.org/documentation/file-format-content/format33/sect4.html#HETNAM) and provide chemical name information for the heterogens in the PDB.

HETATM records are records found in the coordinates portion of the PDB (http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#HETATM) and provide the coordinates for the heterogens.

Your PDB should have both.

[Anonymous]

It may be best to post your edited PDB here, so we can check formatting and the like.

[Author]

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