constraints

[Anonymous]

My pose has DNA strands and I am trying to constrain the blunt ends.

Each DNA chain is numbered starting from 1. Why can’t Rosetta find the atoms?

Here is my constraint:

AtomPair C1* 1C  C1* 35D  HARMONIC 12.028 1.00

And here is the error:

[ERROR] Exception caught by JobDistributor for job VGK8_v2_0001Atom ‘C1* 1359’ not found

 

[Anonymous]

Try C1′ instead of C1* and see what happens.  That’s what Rosetta expects the atoms to be named (you can look at Rosetta/main/database/chemical/residue_type_sets/fa_standard/residue_types/nucleic/dna/*params to see what atom names Rosetta expects).  It’s likely the PDB reader has an override to accept * for ‘ for nucleic acids, but that logic doesn’t inform the constraints file reader.

If changing ‘ -> * in the constraints file doesn’t work, try doing it in the PDB, too.

[Anonymous]

Try C1′ instead of C1* and see what happens.  That’s what Rosetta expects the atoms to be named (you can look at Rosetta/main/database/chemical/residue_type_sets/fa_standard/residue_types/nucleic/dna/*params to see what atom names Rosetta expects).  It’s likely the PDB reader has an override to accept * for ‘ for nucleic acids, but that logic doesn’t inform the constraints file reader.

If changing ‘ -> * in the constraints file doesn’t work, try doing it in the PDB, too.

[Anonymous]

Try C1′ instead of C1* and see what happens.  That’s what Rosetta expects the atoms to be named (you can look at Rosetta/main/database/chemical/residue_type_sets/fa_standard/residue_types/nucleic/dna/*params to see what atom names Rosetta expects).  It’s likely the PDB reader has an override to accept * for ‘ for nucleic acids, but that logic doesn’t inform the constraints file reader.

If changing ‘ -> * in the constraints file doesn’t work, try doing it in the PDB, too.

[Anonymous]

Using C1′ rather than C1* worked. 

Thanks!

[Anonymous]

Using C1′ rather than C1* worked. 

Thanks!

[Anonymous]

Using C1′ rather than C1* worked. 

Thanks!

[Author]

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