The problem hasn't been solved
I am running a docking_protocol for two proteins. Inspecting the score.sc file, I find that the columns Fnat and Irms are "nan" (Not A Number, I suppose). Why could this be happening? I can post more details if needed.
(BTW, what does Fnat mean?)
Dear friends,
I am trying to use “ddg_monomer.linuxgccrelease” in our university cluster.
However, since my protein is too large (a dimer, each monomer contains 663 residues), the calculation ends because of the wall-time (72 hours) before it finishes.
I am here to ask if it is possible to restart the program. Or is there a method to make the program faster, like using MPI?
Thanks.
Hi,
I want to do docking antibody-antigen complex. Understanding from literature, ensemble docking and snug dock is better for Ab-ag. But I didn’t find a complete tutorial or documentation for snug dock. I found just the page in the following link that is some confusing:
https://www.rosettacommons.org/docs/latest/application_documentation/antibody/snugdock
Hello,
I am using Rosetta 15.31 for antibody modeling. when I run the following command:
This is the command I am trying to execute (taken from here: https://www.rosettacommons.org/docs/latest/application_documentation/ana..., in the Preminimization of the Input Structures paragraph, in High Resolution Protocol):
Dear PyRosetta staff,
I'm using your set_bb_true_range() method of the MoveMap class to define the mobile degrees of freedom for some loop. Then, I use a MinMover (min_type="dfpmin") to minimize the loop according to some score function. I want that both backbone dihedral angles (PHI and PSI) were frozen at the Nt end. Unfortunately, it seems that PyRosetta only freezes the PHI angle while keeping mobile the N-terminal (Nt) PSI. In the C-terminal end, the PHI angle is mobile and the PSI is frozen.
Hi,
I had previously run InterfaceAnalyzer in Rosetta 3.5 but then had to re-run it with a more recent version (2015.19.57819) and was surprised to notice that the dSASA numbers were quite a bit different. This is not a calculation I expected to change much and it shouldn't depend on scoring functions.
I just ran the following on 1brs in the integration tests folder:
Hello everyone,
I was running Abinitio protocol and I have noticed that a certain sequence yield sequeced models (S_000001, S_000002, S_000003) in the absence of the secondary structure predicition file. Conversely, in the presence of this file in the protocol some models where not generated (or, at least, not recorded). In fact, I have something like the sequence: S_00002, S_00009, S_00013, etc. From 100,000 models required only around 10,000 were possible to be extract. Is there any resonable reason for this fact?
I have multiple X-ray structures (PDB files) of the same protein. All of them have missing stretches of residues. I want to use all of them to build a single model, with as little missing residues as possible. How can I do this?
Dear Sir/Madam,
I was wondering if there is a tool inside Rosetta that lets me convert a fragment (9-mer for instance) taken from the fragment file of 9-mers into a PDB-like format file.
Any suggestions/information?
Thank you,
Jad