3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: ezequieltijerina13 on November 29, 2017, 12:06:10 pm

Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · Reproduce DSSR · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Title: HADDOCK run could not be processed
Post by: ezequieltijerina13 on November 29, 2017, 12:06:10 pm
Hello , I am having difficulty uploading a file to HADDOCK. I keep receiving an email that states "PDB file is incorrectly formatted. Is there any way I could fix the problem? I have attached the file to this message.
Title: Re: HADDOCK run could not be processed
Post by: xiangjun on November 29, 2017, 12:26:31 pm
Thanks for posting on the 3DNA Forum!

Where/how did you get the dna.pdb file you attached?

Could you please try the attached dna-new.pdb file and report back if it works?

Best regards,

Xiang-Jun
Title: Re: HADDOCK run could not be processed
Post by: ezequieltijerina13 on November 29, 2017, 01:21:55 pm
I submitted the file you sent me to HADDOCK and now the emails says "Second pdb file contains an unknown amino acid or nucelic acid base DT". Make sure to use three letter code for bases and amino acid. I got this file from 3D-Dart. I have attached two file to this email. The file under the name of "DNA- new" is the file you sent me a while ago and the file with the name of "DNA" is the original file. Please help me out with this problem.
Title: Re: HADDOCK run could not be processed
Post by: xiangjun on November 29, 2017, 01:44:40 pm
DT is a standard nucleic acid base name for T in DNA, as of PDB format v3.x (if I remember it correctly). So the error message from HADDOCK means that it is strict (picky) with its input of PDB format. As a test, you may download the DNA structure (e.g., 355d) from the RCSB PDB, and submit it to HADDOCK to see what happens.

I've re-created a new version of the PDB filedna-new2.pdb (attached) for you to try: it has T instead of DT etc.

Best regards,

Xiang-Jun


As a side note, such HADDOCK-related questions are better directed to its creators/maintainers. They know exactly what PDB format they support, and may provide you some working examples.

Title: Re: HADDOCK run could not be processed
Post by: ezequieltijerina13 on November 29, 2017, 04:38:35 pm
Hello, I'm very thankful for you help ,but there is still an error. "It says incorrectly formatted and please align the columns of your PDB properly". I'm not sure how to fix the problem. I have attached all 3 pdb files. DNA.pdb being the original file, dna-new.pdb being the first file you sent me and finally dna-new2.pdb being the final file you just sent me.
Title: Re: HADDOCK run could not be processed
Post by: xiangjun on November 29, 2017, 04:47:20 pm
Thanks for your followup. However, it won't be fruitful to keep trying an unknown target. As mentioned in my previous response, you need to contact the HADDOCK developer to know exactly WHAT PDB format it needs.

At the very least, do you have any example PDB file that works with HADDOCK? I also suggested you try a DNA structure (e.g., 355d) downloaded from the RCSB PDB. The two PDB files I attached can be read without problems by Jmol/PyMOL.

Sorry, I cannot be of any further help other than what I've suggested above.

Xiang-Jun

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.