help surface_docking peptide on ice

Hello everyone,

I am trying to use Rosetta surface_docking protocol to dock a 12 residues peptide on an ice slab.

I tried different formatting options of the input ice – peptide PDB file, but the software crashes.

After looking at the existing (Unsolved) posts on the forum, I created a PDB file formatted in this way:

HETATM    1  O   HOH B   1       1.270   1.866   3.334  1.00  0.00           O

HETATM    2  H1  HOH B   1       1.748   1.514   2.585  1.00  0.00           H

HETATM    3  H2  HOH B   1       1.737   1.530   4.096  1.00  0.00           H

HETATM    4  O   HOH B   2       5.229   4.527   1.023  1.00  0.00           O

HETATM    5  H1  HOH B   2       5.679   4.822   1.816  1.00  0.00           H

HETATM    6  H2  HOH B   2       5.229   3.576   1.080  1.00  0.00           H

HETATM    7  O   HOH B   3       6.581   5.390   3.309  1.00  0.00           O

HETATM    8  H1  HOH B   3       6.548   6.357   3.334  1.00  0.00           H

HETATM    9  H2  HOH B   3       6.136   5.122   4.109  1.00  0.00           H

HETATM   10  O   HOH B   4       5.328   4.574   5.652  1.00  0.00           O

HETATM   11  H1  HOH B   4       5.284   3.613   5.659  1.00  0.00           H

HETATM   12  H2  HOH B   4       4.415   4.853   5.646  1.00  0.00           H

……

ATOM   5293  N   ASP A1765      10.225  49.832  41.655  1.00  0.00           N  

ATOM   5294  CA  ASP A1765      11.689  49.832  41.655  1.00  0.00           C  

ATOM   5295  C   ASP A1765      12.113  49.832  43.137  1.00  0.00           C  

ATOM   5296  O   ASP A1765      11.305  49.832  44.064  1.00  0.00           O

ATOM   5297  CB  ASP A1765      12.241  51.058  40.929  1.00  0.00           C

ATOM   5298  CG  ASP A1765      13.676  50.860  40.536  1.00  0.00           C

ATOM   5299  OD2 ASP A1765      14.406  49.934  40.852  1.00  0.00           O

ATOM   5300  OD1 ASP A1765      14.143  51.881  39.793  1.00  0.00           O

ATOM   5301  HA  ASP A1765      12.021  48.896  41.191  1.00  0.00           H

ATOM   5302  HB1 ASP A1765      12.173  51.951  41.561  1.00  0.00           H

……

(PDB file is also attached)

The command I am using:

/home/oasis/Enrico/installed_software/rosetta_bin_linux_2018.48.60516_bundle/main/source/bin/surface_docking.static.linuxgccrelease -database /home/oasis/Enrico/installed_software/rosetta_bin_linux_2018.48.60516_bundle/main/database -in:file:s start_ice_peptide_1.pdb -include_surfaces -nstruct 10 -in:file:surface_vectors vectors.surf -in:file:frag9 9mers -in:file:frag3 3mers -in:ignore_waters ‘false’ -multiple_processes_writing_to_one_directory

Please note the option -in:ignore_waters ‘false’ that I included, following some suggestions in the previous posts.

The software crashes after a series of core.kinematics.FoldTree calls:

core.kinematics.FoldTree: delete_jump_seqpos: renumbering jump 898 to 867

core.kinematics.FoldTree: delete_jump_seqpos: deleting jump 868

core.kinematics.FoldTree: delete_jump_seqpos: renumbering jump 897 to 868

core.kinematics.FoldTree: delete_jump_seqpos: deleting jump 869

core.kinematics.FoldTree: delete_jump_seqpos: renumbering jump 896 to 869

core

I also tried other PDB formatting styles, and other surface_docking options, but I keep getting crashes!

I am quite sure that my installation is fine, because I was able to complete the surface_docking tutorial.

Also, I think that my peptide and 3mers and 9mers files are fine, since I was able to fold the peptide alone with AbinitioRelax.

So, I think that the problem is the format of the ice structure.

If you are willing to help, and need the other input files, please ask me, I will send them by email, but they are too big for this forum!

Thank you for your attention!

Enrico