Protein-DNA docking SP6

when i perform protein DNA docking using easy interface but it is showing this error Please align the columns of your PDB properly what it really means to

The PDB format is strict about columns ordering.
You must have messed it up modifying the file… Compare the columns with a proper PDB file.

When manipulating PDB files, consider using some of our pdb-tools scripts:


Thank you sir i just now compare my file with a PDB file but still it is showing problem as the above, i am trying to upload my PDB file but it is showing new users can not upload attachments, please have a look if possible solve it out.
Thank you sir!

Then something is still wrong… how did you generate it? How did you edit it?

Try reading it in Pymol and exporting it then as PDB format

After exporting from pymol i found these types of error
There was an inconsistency in your data

Error message

Second pdb file contains an unknown amino acid or nucleic acid base A

Make sure to use three letter code for bases and amino acid

i generated it by 3D-Dart server

HADDOCK requires a three letter code for the base names.
3D-DART does create HADDOCK ready files…

Check the option on the 3D-DART server to create HADDOCK-ready files and use the proper file (i.e. from the last directory)

Thank you so much sir