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    I don’t think that there are any heavy atoms in the PDB file. The executables which i am using is :- rna_denovo.linuxgccrelease.

    And in rosetta PDB files H’ are marked as H* and the numbering of hydrogens do differ like H5′ is 1H5* and H5” is 2H5*.If this is the problem then the PDB files need heavy modifications??(i think)..Is there any way to modify *params files or any other file in source code itself to make things a bit less complicated?