Hi Rosetta Users,
I know this problem has been discussed in the forum several times, but I still cannot figure out how to do it.
I had a PDB file of a protein that contains a phosphorylated serine (SEP) in it. I can use score_jd2.linuxgccrelease to score the pdb without any problem. But when I try to use relax.linuxgccrelease, there is a segmentation fault error right after the "protocols.relax.FastRelax". I read some old threads in the forum and was told that the patch file for SEP in both full-atom and centroid mode is important. I checked the database and I'm sure that two "ser_phosphorylated.txt" files are present in "main/database/chemical/residue_type_sets/centroid/patches" and "main/database/chemical/residue_type_sets/fa_standard/patches". My command to run relax is as follows:
relax.linuxgccrelease -linmem_ig 100 -use_input_sc -nstruct 1 -relax:fast -relax:constrain_relax_to_start_coords -scorefile relax.fasc -s pLys.pdb -out:prefix relax
Is there anything else that I should do to relax my structure? Thank you!
Unless you're doing something special, (and it doesn't look like you are), FastRelax is a fullatom-only protocol, so the centroid mode parameters aren't necessary.
It's a little hard to say what may be going wrong. I was able to run relax with a SEP-containing protein on my local machine using Rosetta 3.8.
Which version of Rosetta are you using, and are you able to post your input PDB? (If you don't want to post it publically, feel free to PM me about it.) Being able to play around with things on my local machine might help with figuring out what's going wrong.
Thank you for the kind reply. I think I downloaded a weekly release of Rosetta (version 3.8) and there is a timestamp in the file name (rosetta_bin_linux_2017.08.59291_bundle). I've uploaded the pdb files and the error message from relax.linuxgccrelease. Thank you!
So you know, Rosetta's numbered releases (e.g. 3.8 and the like) are really just weekly releases which have been relabeled. The numbered release "Rosetta 3.8" and the weekly release "2017.08.59291" are the same.
Using exactly your commandline with the pdb you provided, with Rosetta 3.8, I was able to run relax successfully without any errors.
At this point, I'm thinking that there might be some sort of corruption in your compile of Rosetta. Since it looks like you downloaded the pre-compiled binaries, I'd recommend re-downloading it, and re-extracting it to a fresh directory. This may solve the corruption issues, if they were introduced during the download process.
If that doesn't work, it might be an issue with the precompiled binaries not being compatible with your machine. To fix that, I would reccommend deleting the entire contents of your main/source/build directory and (re-)running the compilation locally. You can find instructions on how to do a local compilation at https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation