# Protein-DNA docking SP6 **URL:** \ **Category:** HADDOCK\ **Created:** [September 18, 2019, 12:21pm UTC](https://ask.bioexcel.eu/t/protein-dna-docking-sp6/1687 "2019-09-18T12:21:34Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![satya22](https://avatars.discourse-cdn.com/v4/letter/s/da6949/32.png) [@satya22](https://ask.bioexcel.eu/u/satya22)\ **Post date:** [September 18, 2019, 12:21pm UTC](https://ask.bioexcel.eu/t/protein-dna-docking-sp6/1687/1 "2019-09-18T12:21:34Z")
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 ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [September 18, 2019, 2:11pm UTC](https://ask.bioexcel.eu/t/protein-dna-docking-sp6/1687/2 "2019-09-18T14:11:59Z")
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](http://github.com/haddocking/pdb-tools) ---
**Author:** ![satya22](https://avatars.discourse-cdn.com/v4/letter/s/da6949/32.png) [@satya22](https://ask.bioexcel.eu/u/satya22)\ **Post date:** [September 19, 2019, 4:48am UTC](https://ask.bioexcel.eu/t/protein-dna-docking-sp6/1687/3 "2019-09-19T04:48:00Z")
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! ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [September 19, 2019, 6:03am UTC](https://ask.bioexcel.eu/t/protein-dna-docking-sp6/1687/4 "2019-09-19T06:03:00Z")
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 ---
**Author:** ![satya22](https://avatars.discourse-cdn.com/v4/letter/s/da6949/32.png) [@satya22](https://ask.bioexcel.eu/u/satya22)\ **Post date:** [September 19, 2019, 6:23am UTC](https://ask.bioexcel.eu/t/protein-dna-docking-sp6/1687/5 "2019-09-19T06:23:38Z")
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 ---
**Author:** ![satya22](https://avatars.discourse-cdn.com/v4/letter/s/da6949/32.png) [@satya22](https://ask.bioexcel.eu/u/satya22)\ **Post date:** [September 19, 2019, 6:24am UTC](https://ask.bioexcel.eu/t/protein-dna-docking-sp6/1687/6 "2019-09-19T06:24:43Z")
i generated it by 3D-Dart server ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [September 19, 2019, 6:37am UTC](https://ask.bioexcel.eu/t/protein-dna-docking-sp6/1687/7 "2019-09-19T06:37:24Z")
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) ---
**Author:** ![satya22](https://avatars.discourse-cdn.com/v4/letter/s/da6949/32.png) [@satya22](https://ask.bioexcel.eu/u/satya22)\ **Post date:** [September 19, 2019, 7:03am UTC](https://ask.bioexcel.eu/t/protein-dna-docking-sp6/1687/8 "2019-09-19T07:03:24Z")
Thank you so much sir