Loop modeling with constraints

[Anonymous]

Hi,

I am trying to model a loop with a constraints file (the constraints are for the atoms of the loop).

but every time I get this message:

[FILE]: src/core/pose/util.cc

[LINE]: 704

[START_MESSAGE]

Atom 'OVL1 31' not found



[END_MESSAGE]

[END_CRASH_REPORT]

 

I also tried to set the flag “-constraints:named” to true but it didn’t help…

I am using the following command:

loopmodel.linuxgccrelease -ex1 -ex2 -extrachi_cutoff 0 -loops:remodel perturb_kic -loops:refine refine_kic -constraints:named true -loops:fix_natsc -in:file:fullatom -in:file:s my_file.pdb -loops:loop_file my_loop_file -nstruct 1 -constraints:cst:file my_const -constraints:cst_weight 1.0 > loop_model.log

 

Is there any way to model a loop in rosetta with a constraints file (without constraints it work fine)? 

thanks!

[Anonymous]

Hi, 

could you post the constraints file? Is it possible that atoms are removed from the input pose, and the constraints are not referring to the atoms you intended to?

Amelie

[Anonymous]

Hi,

I am uploading the constraints and input files.

I will mention that this happenes for me every time with different input structures and different constraints files.

 Thanks for the help!

 

[Anonymous]

Any idea on  how to resolve this?

Thank you very much!

 

[Author]

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