# ROSIE

Rosetta Server

## Fv modelling Job Mab_Top 「№33253」

Category:
ROSIE

Hi all,

I am having problems using the ROSIE antibody section for comparative modelling of a Fv fragments, job number 33253 (Mab_Top).
Previous attempents have failed, and now I made a modification on the N-terminus (because this is was not fully sequenced) and the job is flaged as finished altough without any structure, as well as without reports of potencial errors.

I guess that there was any problem with the modelling since the CPU time used was so small 0.0147222222222.

Post Situation:

## Numbering failed

Category:
ROSIE

Job ID 32176 failed with this error:

ERROR: FR_L3 length 28 is not between 32 and 34
Numbering failed.  Exiting.

Any ideas on how I can remedy this? Thank you

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## weights for pH_protocol

Category:
ROSIE

Dear all,

I have been recently testing pH_protocol to calculate the pKa of one of my proteins. In the original paper, the authors include the weights function to be used with the protocol:

fa_atr 0.8

fa_rep 0.44

fa_sol 0.65

fa_intra_rep 0.004

fa_dun 0.56

hbond_lr_bb 1.17

hbond_sr_bb 1.17

hbond_bb_sc 1.17

hbond_sc 1.1

hack_elec 1.0

e_pH 1.0

ref 1.0

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## Sequence Tolerance Failed

Category:
ROSIE

Dear all,

I submitted six jobs to Rosie (28069 through 28074) under the username dstork. They failed quickly with no error messages beyond "Failed * Tech support has been notified of this error" anywhere that I can see. After waiting a few weeks the issue hasn't been resolved. What can I do to get this job to work?

Thanks,

-Devon

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## peptiderive problem

Category:
ROSIE

Hello

My attempts to submit a job in peptiderive server become fail. I cant submit any job in peptiderive server but I am getting no input error job in this server.

Thank you

Fatemeh

Post Situation:

## Ligand docking error Could not find essential file trigger-00001.ligand_docking_protocol

Category:
ROSIE

Hello,

My attempts at ligand docking on Rosie (e.g. job 26146)  keep failing after less than 15min. I am getting no input error. The json logs return the error:

  "log": "\nCould not find essential file trigger-00001.ligand_docking_protocol/score.sf in DB!\n",

I used Frog2 to generate my ligand sdf file and Chimera to estimate the starting x,y,z coordinates.

Any hints at what I might be doing wrong?

thanks,

Isabelle

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## chothia numbering error of FR_L1

Category:
ROSIE

I submitted a Heavy and lIght chain sequence with and without the 'multiple template grafting' and H3 loop modeling and recived the same errors each time- "Chothia numbering of FR_L1".

Does anyone know how to get around this error so that the antibody will be modeled? job #'s 24670, 24671

thank you

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## supercharge problems

Category:
ROSIE

Dear Professor Bryan Der,

Thank you very much for your great server. I've come across two essential questions using your techniques and I really need your help so I can continue working on my PhD thesis.

I've used both supercharge methods:

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## CDR are not being recognized

Category:
ROSIE

Hi!!

I had been suscesfully using ROSIE to generate Fab models for a while and lately the server has not able to recognize the CDRL3 and CDRH3 in my antibody sequences. I also tried a sequence that was previously used and modeled but now the server gave an error

ERROR: CDR L3 cannot be recognized !!!  L3 pattern: C[A-Z]{1,15}(L|F|V|S)G[A-Z](G|Y)

and I dont undestand why  the CDR cant not be recognized now. The pattern of the input seqeunces looks correct.

I would really aprreacite some help in this matter

Post Situation: