Snugdock

[Anonymous]

I have been running snugodck jobs on Rosie for a while but queue times are long so I am trying to run jobs locally.   I am getting the error below:

 

ERROR: Sequence for partner1:

EVQLVESGGGVVQPGRSLRLSCAASGFTFDRYGMHWVRQAPGKGPEWVAVISHDGSHEEYADSGKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDGAYYYDYSGYPYDYNGIDVWGQGTTVVVSSALTQPHSASGPPDQTVTISCSGSSSNIEGNTVNWYQQFPGKAPQLLIYGKDQRPSGVPDRFSASKSGTSASLTISGLQAEDEADYYCAAWDDSLNGWVFGGGTKLTVLGQ

 does not match first member of ensemble1:

SALTQPHSASGPPDQTVTISCSGSSSNIEGNTVNWYQQFPGKAPQLLIYGKDQRPSGVPDRFSASKSGTSASLTISGLQAEDEADYYCAAWDDSLNGWVFGGGTKLTVLGQEVQLVESGGGVVQPGRSLRLSCAASGFTFDRYGMHWVRQAPGKGPEWVAVISHDGSHEEYADSGKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDGAYYYDYSGYPYDYNGIDVWGQGTTVVVS

 

Prepack runs fine using:

../main/source/bin/docking_prepack_protocol.macosclangrelease -in:file:s 136C_1.pdb -ex1 -ex2 -partners LH_EFG -ensemble1 antibody_ensemble.list -ensemble2 antigen_ensemble.list -docking:dock_rtmin

 

 

For snugdock I am using:    (only 5 structures just to see if it is working):

../main/source/bin/snugdock.macosclangrelease -s 136C_1.pdb -ensemble1 antibody_ensemble.list -ensemble2 antigen_ensemble.list -antibody:auto_generate_kink_constraint -antibody:all_atom_mode_kink_constraint -partners LH_EFG -spin -dock_pert 3 8 -ex1 -ex2aro -nstruct 5

 

The error says that sequence for partner 1 is the heavy chain, but in the PDB files the light chain is first.

[Anonymous]

Hi,

Can you check via a TextEditor (this is important because PyMOL will order chains alphabetically) whether or not the prepacked files listed in “antibody_ensemble.list” have the same order as the file “136C_1.pdb”? 

Due Rosetta’s internal representation, all the files have to have the chains in the same order and this order has to match the “-partners” flag.

Best,

Jeliazko

[Anonymous]

Jeliazco,

I checked all the files by texteditor and they all are L followed by H.  FYI – attached are a prepacked file from the antibody_ensemble.list, and also the partner1_starting_conf file, and 136C_1.pdb (I truncated the antigen part so that file is less than 512KB limit for uploading).  (I put txt as the file extension since ppk cannot be uploaded).

 

136C_1.pdb is an output file from a snugdock run on the ROSIE server.  136C_1.pdb is fine as input when I use snugdock on the ROSIE server.

 

Thanks very much for your help.

[Anonymous]

Dear Mike,

First, sorry about the long wait. I was sick and then traveling for the holidays. Looking at these files, the command line you described should work, so I am surprised.  I did not know about the upload limit on the forum. I would like to try to replicate the error on my machine. Would you mind emailing everything necessary to do so?

You can contact me at jeliazkov@jhu.edu.

Best,

Jeliazko

[Anonymous]

Jeliazko,

 

Thanks very much.  I will send you everything by email.

In the meantime I have been running snugdock with just a single antibody and antigen, without ensembles, on a local platform.   I am trying to repeat a fast snugdock trial that I ran previously on Rosie, to make sure that I get similar results.  I use the snugdock commands given above but without the ensemble commands.  The runs finish but I find that the range for Irms is much larger than for the fast snugdock run on Rosie.   What flags corresponds to fast snugdock on Rosie?

 

Thanks,

Mike

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