polymer docking using rosetta scripts

[Anonymous]

 

   Hi  My name is  Jong hui Hong

   I’m trying to dock the ligand which has 5 chemical linked via covalent bond( ACE-UB4-DPP-GLY-GVE) using Rosetta-Scripts

   I changed ligand residue name into PRD and made conformer using obabel , made paramter file using molfile_to_params.py without any problem

   but when I run docking using  rosetta_scripts.linuxgccrelease

  I got the following error

  [ ERROR ] UtilityExitException

ERROR: Non-virtual heavy atom  C7  is missing in rotamer library for residue PRD!

 

   I couldn’t figure out what is the problem even I searched a lot in google.

  Here is my option file for running rosetta_scripts

 -in:file:s crystal_complex.pdb

-in:file:extra_res_fa PRD.params

-out:path:all dock_res

-out:file:scorefile score_6wuuA_PRD.sc

-nstruct 10000

-packing:ex1

-packing:ex2

-packing:no_optH false

-packing:flip_HNQ true

-packing:ignore_ligand_chi true

-parser:protocol dock_p.xml

-mistakes:restore_pre_talaris_2013_behavior true

-qsar:max_grid_cache_size 1

 and docking protocol file ‘dock_p.xml’ is attached

  Any kind of suggestion would be welcomed for above error.

  Thanking in advance for helping me

  Regards

  Jonghui

 

 

[Anonymous]

That error message (“Non-virtual heavy atom  C7  is missing in rotamer library for residue PRD”) means that you have a C7 atom listed as being present in the PRD.params file, but the associated conformer file (listed in the PDB_ROTAMERS line in the PRD.params file) has an entry which is missing that atom.

My guess is that there’s some issues with the multiple conformers you have in the original input SDF/MOL2 file you passed to molfile_to_params.py — If one of the conformers in that file didn’t have all the atoms the other did (or if one of them has different atom ordering, etc.), then the molfile_to_params.py file may generate something which may give that error.

I’d make sure that all the conformer entries in that SDF/MOL2 file are of the same structure, and are layed out similarly. (You can check this by opening the SDF/MOL2 file in most molecular viewers — they should allow you to cycle through the multiple conformations in the file.)

 

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