I have used Modeller to to produce linear peptide. When I refine the linear peptide using relax protocol an peptide with for instance AAA is shorted to AA. How do I prevent this from happening. I am using relax.linuxgccrelease -database /home/knut/rosetta/rosetta_database -in:file:native $f -out:prefix relaxed_ -out:nstruct 1 this command with these options.
It's probably deleting residues as it reads the PDB in. Check your input file to ensure:
A) all atoms have nonzero occupancies,
B) all residues have the four backbone heavyatoms defined (N, CA, C, O)
If those two things are both true, attach the PDB and I'll see if there's a problem I can spot.
I have added the a peptide which contain 3 A residues. The atoms have nonzero occupancies and ot contain N,Ca,C and O.
Your first residue has atoms with zero occupancy (2nd to last column).
Those peptide are build using abinito. Is there any way to set the occupancy to 1 for several thousand pdb?
sed or awk would be the fastest way. I'm not enough of an awk master to give you the command but awk will do it with a carefully crafted command line. In sed, try something like:
sed "s/0.00 /1.00 /g"
on all your filenames. (This will also set your B-factors to 1; you can learn sed/awk and regular expressions if you want to change only the occupancies column.)