The problem hasn't been solved
Hi everyone
I'm beginner of ROSETTA/Linux commandline, so please explain problems easily
I can model protonated histidine residue(HIS_P?) by docking_prepack application
I am trying to design a helical linker between two strongly interacting subunits that connects their termini using RosettaRemodel.
I am running remodel with the following flags in mpi mode and get the desired output (around 2-4 structures with -num_trajectory 32). However when I increase -num_trajectory to e.g. 1000 I still get only around 2-4 strucures out (named 1.pdb 2.pdb ...). while computation time increases drastically.
First, I'm sorry for my poor english.
I compiled rosetta applications via mpi options
(/home/ael/Desktop/rosetta_bin_linux_2020.28.61328_bundle/main/source/bin/relax.mpi.linuxgccrelease)
and I tried to use relax application to prepare structure
Then, when i start relax application, my cpus (16cores, 32threads) rus fully and it calculates same calculations 32times
(one output pdbs and 32 scores in .sc file)
how can i solve this problems?
Hi,
I'm using next-generation kIC to model one loop , which interacts with another subunit in the hetero-trimer complex.
I'd like to input the whole 3-chain structure for loop modelling as adjacent subunit could stabilize the loop conformation because of the interaction.
But I've got no idea where I can designate the chain for loop modelling if I input multi-chain structure?
Could anyone please give me some ideas?
Thanks a lot,
Tianyang
Hi everyone,
I detected an issue with the small molecule-docking application using rosetta scripts and the setup for doing large-sized libraries screening. In this set up you generally use a "screening_job_file" input that specifies which combination of ligand and protein structures will be used during the simulation. This file looks something like this:
Good evening, I want to use the pepspec anchor dock application and I am using the following flags file:
-ignore_unrecognized_res
-pepspec :: no_prepack_prot
-pepspec :: anchor_type PRO
-pepspec :: prep_align_prot_to input / 1CKA.nopep.pdb
-s input / 1CKA.nopep.pdb
-pepspec :: ref_pdb_list input / homol.pdblist
-restore_pre_talaris_2013_behavior
-score :: weights pre_talaris_2013_standard.wts
-pepspec :: soft_wts soft_rep.wts
-pepspec :: interface_cutoff 6
-pepspec :: n_dock_loop 1
Hello,
I have recieved this warning when trying to use FlexPepDocking refinement protocol for a tyrosine phosphorylated peptide.
core.util.switchresiduetypeset: (0) [ WARNING ] When switching to centroid mode, a normal replacement type for residue TYR:phosphorylated can't be found.
core.util.switchresiduetypeset: (0) [ WARNING ] an autogenerated replacement type is being used instead.
Hi all,
I am trying to run the Pepsec demo and I got the following error:
ERROR: Unable to open weights/patch file. None of (./)standard.wts or (./)standard.wts.wts or /mnt/d/Softwares/Rosetta/rosetta_src_2020.08.61146_bundle/main/database/scoring/weights/standard.wts or /mnt/d/Softwares/Rosetta/rosetta_src_2020.08.61146_bundle/main/database/scoring/weights/standard.wts.wts exist
ERROR:: Exit from: src/core/scoring/ScoreFunction.cc line: 3461
Good evening, I would like to ask for your help because I am trying to run the pepspec anchor dock protocol, so I am using the following options as flags, which come in the tutorial: