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Help on converting regular PDF file to HADDOCK-ready file


I am a new user. I was trying to use the HADDOCK. The ligand is an ssDNA of 22 nucleotides, with a particular secondary structure. The NMR structure is available in the PDB database. I tried to manually change the 2-letter code, such as "DT", in the original PDB file into 3-letter, such as"THY". However, the modified PDF file could not even produce the normal structure in PyMol, nor could be accepted by the HADDOCK server.

There may be a solution existing. As a new user, I would appreciate a lot if anyone could advise me what to do.

Basically, there is no need to generate a new model for this 22-mer ssDNA, since the structure is available. It is how to convert its PDF file to the one that still gives the same, original structure, but can be accepted by HADDOCK for docking.



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