loop modeling

[Anonymous]

Hi,

I am trying to mutate the residues of a loop using resfile but it seems that the rosetta doesn’t read the resfile at all. I checked this by adding a random sentence and ran the job, which ran perfectly but with native loop sequence. Here are the options which I used for loop modeling:

flag file:

-database /home/rosetta_mpi/rosetta_database
-loops:remodel perturb_ccd
-loops:refine refine_ccd
-ex1
-ex2
-resfile resfile.txt
-loops:input_pdb pA.pdb
-in:file:fullatom
-loops:loop_file loopfile
-loops:frag_sizes 9 3
-loops:frag_files aat000_09_05.200_v1_3 aat000_03_05.200_v1_3
-out:file:fullatom
-nstruct 10
-overwrite
-in:file:native f_native.pdb

loop file:
LOOP 129 139 134 0 1

resfile (with error):
NATRO
START
129-137 A PIKAA GS
129 A PIKAA GS
130 A PIKAA GS
131 A PIKAA GS
132 A PIKAA GS
133 A PIKAA GS
134 A PIKAA GS
135 A PIKAA GS
136 A PIKAA GS
137 A PIKAA GS

resfile (without error):
NATRO
START
129 A PIKAA GS
130 A PIKAA GS
131 A PIKAA GS
132 A PIKAA GS
133 A PIKAA GS
134 A PIKAA GS
135 A PIKAA GS
136 A PIKAA GS
137 A PIKAA GS

Can anybody tell me what could be reason for not getting mutations according to resfile. I am using rosetta 3.4.

[Anonymous]

It looks like the CCD method doesn’t allow mutation. (Which makes some sense, as the fragments used during CCD are sequence-specific.)

If you use refine_kic instead, the resfile should be used for mutational purposes.

[Author]

Posts