How to remove clashes in peptide bonds and proline residue?

[Anonymous]

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

[Anonymous]

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/d7d/app_idealization.html) first, then relax. Relax is almost certainly not altering angles and lengths, only torsions.

[Anonymous]

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.

[Author]

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