How do I implement more CPU cores in the execution of FlexPepDock?
Hello all. I am a university student currently doing my thesis, and I really don't know if this topic has been adressed before, but I couldn't find anything like my question.
Hello all. I am a university student currently doing my thesis, and I really don't know if this topic has been adressed before, but I couldn't find anything like my question.
Hi,
I performed a protein-protein docking within rosetta by using a single receptor structure and several conformations of the same ligand protein. Now I am trying to cluster the results (aprox 1000 structures) using the cluster application included in rosetta by running:
cluster.linuxgccrelease -in:file:l pdblist -in::file::fullatom
Hi all
Recently I'm now doing large scale protein ligand docking using rosetta
while I'm doing , I got the following warning not error
On April 3, I submitted three identical jobs listed below:
21428
21427
21425
I want to cancel the jobs but when I hit “Cancel” nothing happens. How can I kill these jobs?
I ran the below command for docking ;
I ran the below command for docking ;
Hello everyone!
I am getting this following error when I am trying to run a rosettaDNA application program in which i want to change the specificity of a protein so that it binds to a target DNA. In most published articles, I have seen "hack_elec 0.42 " or similar values. However, it's not working in my case. Can you help me with this?
Hey guys, I counterpart with problems as topic saying:
First, I want to use others computational results as reference to optimized docking option, so I have to relax them into same scorefunction, meanwhile relax the inputs which generate from different methods for better results and avoid disulfide bonds error due to different scorefunction, right?
Hello all,
I have been trying to dock a library of ligands to a protein while following the Meiler lab tutorials. While I have been able to prepare most of the prerequisite files, I am unsure how I am supposed to obtain 'crystal_complex.pdb'. Trying to download the protein bound with a ligand .pdb file from the protein data bank and using that as my crystal_complex.pdb does not seem to work. While it seems that options.txt and dock.xml have been set up correctly, protein complex.pdb is the only thing preventing me from running the docking itself.
Hello!
I was a little bit confused about what exactly the stub libraries are and how we are supposed to generate them. From what I understand, they're simply just disembodied residues that we consider "important" to the interface in the docked complex. So, are the stub files just generated by taking a protein structure and deleting everything except for the hotspot residue, then saving that singular residue as a PDB file? Also, is it possible to assign hotspot residues to both chains that we are docking together?
Thank you so much.