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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: 

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 

 

Post Situation: 

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

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

Post Situation: 

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

Post Situation: 

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