Unsolved

Hi,

I wanted to model two tight turns in my protein keeping the backbone of the protein fixed. This was done to evaluate the change in the energy due to changes in loop sequence and also to look for low energy conformations. I wanted only some selected residues at those loop positions for which I made a resfile.

Here are the parameter for loop modeling :-

-loops:refine refine_kic
-loops:input_pdb 1gfl.pdb
-loops:loop_file loop_file.loop
-in:file:fullatom
-in:file:native 1gfl.pdb
-resfile : resfile
-ex1
-ex2
-loop:fix_natsc
-loop:refine_repack_cycles

Hi,

I want to use a crystal structure with a shorter protein sequence as my native structure during loop re-modelling so the rmsd of generated structures will be aligned to it. But there is always an error:

ERROR: Start pose and native pose don't match in length
ERROR:: Exit from: src/protocols/loops/LoopRelaxMover.cc line: 222

How to force to align the same region of the two structures?

Many thanks.

Hello,

I used rosetta3.3 to refine loops in my protein. And the command I used is

loop -loops::input_pdb protein.pdb -loops::loop_file protein.loop_file -loops::frag_sizes 9 3 1 -in::file::fullatom -loops::frag_files protein_aat000_09.200_R3.gz protein_aat000_03.200_R3.gz none -loops::random_loop -loops::refine refine_kic -abinitio::rerun 1 -abinitio::start_native -database $database -out:nstruct 100 -ex1 -ex2 >loops.log

But among the output files there is no scorefile (loops_output.sc)

Does anyone know if the pair term has changed since it's introduction? Does it use the same pdb statistics and bins as described in:
Simons, K. T., Ruczinski, I., Kooperberg, C., Fox, B. A., Bystroff, C. & Baker,D. (1999) Proteins Struct. Funct. Genet. 34, 82–95.

It seems as though the term is the same for centroid and full-atom scoring. Is this true?