Protein-DNA docking SP6

HADDOCK
1

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

2

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:

See http://github.com/haddocking/pdb-tools

3

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!

4

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

5

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

6

i generated it by 3D-Dart server

7

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)

8

Thank you so much sir