I am trying to use the loopmodel ccd to build a loop region with missing residue positions in the original PDB file.
The whole sequence is of 228 amino acid and the missing region is 223-228.
Can I ask
1) As the loop to be built is at the end of the sequence (i.e. termini), how can I specify the loop file?
If I use "LOOP 222 228 0 0 0", I was told (ccd_1.log attached):
"core.kinematics.FoldTree: FoldTree::reorder( 1 ) failed, new/old edge_list_ size mismatch"
If I use "LOOP 222 228 228 0 0", I was told the same thing (ccd_2.log attached).
It is exciplitly indicated that "quick_ccd can also remodel termini"
So how can I really do this?
2) I am building homology model. I would like to minimize the relax in the rest of the structure (i.e. before residue 223).
I am going to use the options below following "bcorreia" said in
Is this suitable?
# NOT use -loops:extended
-loops:frag_sizes 9 3 1
3) Does "-relax::fastrelax_repeats" exist in the "loopmodel.linuxgccrelease"?
I was told
ERROR: ERROR: Option matching -relax:fastrelax_repeats not found in command line top-level context
when using it.
Thank you very much.