Hi all:
I have got a protein model with clashes in several peptide bonds between O and N atoms, proline residues and some side chanis. The "relax" app removed clashes in the side-chain, but was not able to correct the peptide bonds and proline residues. The following are the options that I used in both fast and throrough runs of the app:
relax.linuxgccrelease -database /home2/rosetta_database -in:file:s 8nC.pdb -relax:fast(thorough) -score:weights score12_full -ex1 -ex2 -nstruct 10
relax.linuxgccrelease -database /home2/rosetta_database -in:file:s 8nC.pdb -in:file:fullatom -relax:fast(thorough) -score:weights score12_full -ex1 -ex2 -nstruct 10
relax.linuxgccrelease -database /home2/simcode/rosetta_database -in:file:s 8nC.pdb -relax:fast(thorough) -score:weights score12_full -ex1 -ex2 -ex1aro -nstruct 10
What should be done to correct the peptide bonds and prolines? Thanks.
Regards,
Anatoly
I'm guessing some of your clashes are due to bad bond angles or bond lengths (molprobity can detect these, I think)? If so, try running idealize (http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d4/d...) first, then relax. Relax is almost certainly not altering angles and lengths, only torsions.
It was a triple problem. Besides the clashes, the structure was in the CHARMM format and had gaps in the residue numbering. I corrected that and then the idealize and relax apps did the rest. Thanks.