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!