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Does the pdb file in the output folder of pKa give us the right protonation state of pdb file?
Also, there are two options in pKa program in ROSEI:
1.Pack side chains and protonation states of the residues neighboring the target residue during pKa calculations
2.Pre-pack the side chains and protonation states of all the residues in the input PDB before pKa calculations
which one should we use to get the right protonation state?
Hi ROSIE and FARFAR2 team,
I used FARFAR2 to test the 3D structure prediction of several RNAs two weeks ago with native PDB uploaded. But all the jobs were finally dead with the error message "2-rescore_to_native_or_lowest". Could you tell me why this happened? You can find the sequence, 2D structure, and native PDB in the attachment.
I am using Rosie antibody server for modeling antibody. In order to validate the model i need to run the PLOT LHOC script on the output results from Rosie server. However while running the script i am only getting the graph for the final model and not the template. kindly can anybody share the comand for running the PLOT LHOC script. Also whether the template used for the calculation by PLOT LHOC is grafted model or the original template PDB.
Dr. Suji george
Our lab is planning to design a web server, and we would like to incorporate one of the binaries and the corresponding Rosetta database in our pipeline.
We would like to incorporate Rosetta's supercharge binary (https://www.rosettacommons.org/docs/latest/application_documentation/design/supercharge) along with the corresponding common database in our web server as a component of our web server pipeline.
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.
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: