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Loop modeling with constraints

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Loop modeling with constraints


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/
[LINE]: 704
Atom 'OVL1 31' not found



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)? 


Post Situation: 
Sat, 2021-03-20 03:53


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?


Sun, 2021-03-21 15:08


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!


Wed, 2021-03-24 02:08

Any idea on  how to resolve this?

Thank you very much!


Thu, 2021-04-08 07:37