Hello
Recently, I am trying to predict flexible tail region of protein by using Floppy tail.
First I tried to use Floppy tail with test data (4tailstestdata.pdb).
I have run Floppy tail as below command
mpiexec -np 4 FloppyTail.mpi.linuxgccrelease -in:file:s 4tailstestdata.pdb -in:file:movemap mapmover -nstruct 4
//movemap
RESIDUE 90 117 BBCHI
RESIDUE 207 233 BBCHI
RESIDUE 324 351 BBCHI
RESIDUE 441 468 BBCHI
and I got 4 pdb files those file and each model has different amino acid sequence.
I couldn't figure out why sidechains mutated during calculation.
Can I disable the sidechain mutation?
| Attachment | Size |
|---|---|
 inputdata | 494.1 KB |
| please remove ".pdb" and extract file as zip | 485.62 KB |
 sequence comparison | 92.14 KB |
Category:
Post Situation:
FloppyTail original forbade mutation. Some users wanted the ability to design, so I put that in. An unfortunate consequence of Rosetta's underpinnings is that if it CAN design, it WILL design by default.
The solution is to add -packing:repack_only to your command line.
I assume this is a test command line for debugging purposes? You do not have nearly enough nstruct or cycles for real modeling.
Hello smlewis
Thank you for giving me good advice.
I should have pay more attention when I read the documentation's General options.
Now, I am running FloppyTail by below command and generating structure with expected sequences without design.
mpiexec -np 4
FloppyTail.mpi.linuxgccrelease
-in:file:s inputstructure.pdb
-in:file:movemap mapmover
-FloppyTail::perturb_temp 0.8
-FloppyTail::perturb_cycles 1000
-FloppyTail::refine_temp 0.8
-FloppyTail::refine_cycles 1000
-FloppyTail::refine_repack_cycles 30
-packing::repack_only 1
--overwrite
-nstruct 300
(Relatively few perturbation and structures compare with nstruct=30000 described in Documentation for FloppyTail)
In my case, tail regions were not seen in crystal structure. So, I think I don't need to generate many structures to find a unique solution.
Your application and advice helped me a lot. Thank you!