The problem hasn't been solved
Hi all,
I'm looking for a basic sanity check on how mpi should work with mp_mutate_relax. I've compiled rosetta-2019.47.61047 with extras=mpi and it all seems to be working fine. So if i run mpiexec -np 4 $rosetta3/bin/mp_mutate_relax.mpi.... with the following flags:
I want to fix (freeze) ligand during fastrelax because the fastrelax changes ligand conformation weirdly .
This happens even with params file of the ligand.
Therefore, I tried ignore_unrecognized_res, but this option just not outputting the ligand in the result file.
Here I attach screenshots.
Thank you
Hi,I want to use ResolutionSwitcher in Montecarlo.cc to relax pdb after stage1-4,when i add "#include<protocols/abinitio/ResolutionSwitcher.hh> in MonteCarlo.cc",it turn to be a error"Resolution switcher was not declared in this scope".
I included all the header files but still not working.
I know the full amino acid sequence for my protein. I have obtained its X-ray crystal PDB structure, as well as the mtz file from the crystallisation. There are several loops and termini not resolved. Can I ask what is the best protocol to predict the missing part? I understand it would still not be fully "true" after Rosetta's modelling. I just want to have a "mostly likely" one that can be used as the starting point for my molecular dynamic simulation.
The tutorial at https://www.rosettacommons.org/demos/latest/tutorials/loop_modeling/loop_modeling says "You can build multiple loops in the same simulation by altering the blueprint file to indicate where these loops are".
I am exactly using the same files in the tutorial of https://www.rosettacommons.org/demos/latest/tutorials/loop_modeling/loop_modeling
In the "Extending the Termini" section, I use "3gbn_missing_cterm.pdb", "3gbn_missing_cterm.remodel" and "flag_missing_cterm" files as input, with a command
$ROSETTA3/bin/remodel.linuxgccrelease @flag_missing_cterm
For outreach, I made a spinning and blinking FITC-labelled Christmas tree (https://michelanglo.sgc.ox.ac.uk/r/christmas) using various Rosetta tools, which I have learnt to use properly thanks to all of you.
So using the excuse of the cheer of the holiday season, I wanted to sincerely thank all of you for all the help I have recieved in this forum! It has been invaluable and I really mean it.
Hello,
I'm docking a small molecule into an enzyme utilizing using match style constraints and the EnzRepackMinimize Mover. The constraint is between my small molecule and a cofactor in the enzyme.
I've generated the params file for both my small molecule and the cofactor. When I run my script with the following distance constraint, everything works fine.
CONSTRAINT:: distanceAB: 1.2 0.1 1000 0 2
When I run my protocol trying to turn on the covalency term as in the following line
I have been running snugodck jobs on Rosie for a while but queue times are long so I am trying to run jobs locally. I am getting the error below:
Hi all
I'm using DARC(Docking approach using ray-casting) to do the blind ligand docking.
In the tutorial of DARC, to include electrostatics calculations, tools from openeye such as omerga were used.
tools in openeye are not free.
Are there similar tool or program to do electrostatics calculation in DARC which is free?
Thanks
Regards