The problem hasn't been solved
I am using the relax.linuxgccrelease application to relax a protein complex. I simply send the pdb containing all of the fomed complex to relax.
The score outputted by relax represents the sum of the score of folding plus complex formation (in Rosetta arbitrary units, of course)?
Dear all,
can I used sequence_tolerance to optimize the binding pocket on a protein for a chemical compounds?
I used molfile_to_params.py to generate a params file for the compound. But I do not know how to feed this to sequence_tolerance?
Thank you for the help.
Dear Rosetta Developers
I'm quite new to Rosetta. Recently, I want to perform a loop modeling using Rosetta. So I want to compile Rosetta-3.5 on our cluster.
[root@c02125 ~]# cat /proc/version
Linux version 2.6.32-220.el6.x86_64 (mockbuild@c6b18n3.bsys.dev.centos.org) (gcc version 4.4.6 20110731 (Red Hat 4.4.6-3) (GCC) ) #1 SMP Tue Dec 6 19:48:22 GMT 2011
Dear all Users,
I want to dock a small molecule (glutathione) on one enzyme? I wonder that can I do with glutathione which is not the peptide.
Could some one explain to me?
Thank you so muc
Phan Vy
Hi all,
I want to get an all atom model of my coarse grained protein structure (after adding all the side chains back). I have been using the repacking algorithm to do so, but unfortunately its not doing the job. The side chains are not packed properly. Can you help me suggesting on how to go from coarse grained protein to get an all atom model for my protein. Is there any minimization protocol that can take care of this. Kindly let me know.
Thank you.
Hi,
I'm using pepspec to design a peptide. I've been able to run the application with some options (listed below) but my peptides always seem to fly off into space, with the exception of the region near the anchor residue. I've tried a few different combinations by looking at the application documentation, but I can't seem to get anything that looks "reasonable". My options are:
-pepspec::soft_wts soft_rep.wts
-pepspec::interface_cutoff 5
-pepspec::clash_cutoff 5.0
Hi Rosetta people
I have an odd problem concerning the interface rmsd output from rosetta dock.
I have two structure outputs from different runs. Only difference is using saxs as restrain in one run otherwise the scripts are identical.
I get better irmsd from the saxs run (0.333 vs. 1.116) but when looking at the structures there is barely any difference, I have checked rotamers as well.
Hi,
I am writting some files using the classes in rosetta,changing *settings files as the readmefile indicated,as a example,i wrote a class calculateTT using classes like Pose,Movemap etc,and when i recompiled it,it showed error as following:
Hi everyone,
I am trying to carry out some docking experiments: I have the structure of my protein in .PDB and then the cofactor NADP in .sdf.
I think that I have some problem with the output: I can only open the structure of the protein and then the .sdf of the cofactor which is not docked.
The main thing you need to know is that I am not an expert at all in this field, and I would be grateful if someone could help me to carry out the docking and visualizing it. Currently, I am using Pymol to visualize structures.
Hello everyone,
I build Rosetta 2015.12 on Scientific Linux 7 (SL-7). And, I follow the protocol of RosettaAntibody3 to do antibody modeling.
(https://www.rosettacommons.org/docs/latest/antibody-protocol.html)
When, I run the script of “antibody.py” through following command as
