The problem hasn't been solved
Fast relax works fine with two ligands when the .params file are provided in the format.
-extra_res_fa LG1.params LG2.params
But when the same protocol is used with a few added flags such as
-relax:respect_resfile
-packing:resfile resfile
it fails with the following message
I have successfully installed PyRosetta via anaconda by command of "conda install pyrosetta" in Linux (Windows subsystem Linux) according to this instruction.
I have been reading some post looking for an anwer to my question but I still not complitely sure about it. I understand that for a complex, what rosetta gives you is a score that it is no exacly the DG. I would like to know if with the next code, using the standard score funcion, I can calculate for a comple of 2 chain the DG with the formula:
DG= Score_complexe - (Score_chain_A + score_chain_B)
I want to graft a coenzyme binding sites to a scaffold, so the first thing is to define a theozyme. However, the exsiting .PDB structures binding the coenzyme are not accessible, what I can download is only protein crystal structure without ligand. I that way, what should i do？ Should i DOCK the ligand to the protein at first? could anyone explain me the procedure? Thanks a lot!
I have tried the latest version of Pyrosetta Anaconda python3.6 (PyRosetta4.Release.python36.mac 2019.19+release 5adc612fd9dee20f808a07e761610d95698b0f35) and previous version, PyRosetta4.Release.python36.mac 2019.18+release on MacOS, but run into the same errors when I do, for example,
Hey,
I want to redesign the interface of two three-fold symmetrical proteins and I thought of using RosettaScripts.
I first wanted to make it work on one three-fold symmetrical protein and then continue with the interaction, but I am stumbling on some errors.
I'm using LinkResidues, because the protein is three-fold symmetrical, so a mutation on residue a should also occur on residue b and c, thus without breaking the symmetry of those residues.
I'm using:
Hello,
I am running Scientific Linux 7.6 64-bit and using python 2.7 trying to install the regular python 2.7 Scientific Linux/Red Hat linux PyRosetta4.
After running setup.py I get the following error:
Hi, I need your help on your experience of the number of structures generated from Rosetta by specifying nstruct:
Have you ever met a situation, for example, you specify nstruct = 100, and Rosetta generates less than 100 structures at the end of the run?
More information:
1) I am using RosettaScripts to design a protein interface. I have specified a cutoff of SASA but I don't think it would affect the final number of structures.
where should I find rosetta scripts to do protein interface design? I want to design interface binding of two docked protein in order to higher binding affinity