HADDOCK Docking with RNA and Protein

HADDOCK
1

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to http://www.bonvinlab.org/software/haddock2.2

Hello,
I am new to using the HADDOCK web-server. I am having an issue with potassium cations in the pdb of my RNA structure. The potassium ions are needed for stability of the RNA structure, so I’d like them to be present for docking.
The error I am receiving says:
There was an inconsistency in your data
Error message
First pdb file contains an elemental ion K without specified charge.

Is there an example online of how my potassium cations should be specified in the pdb file? I am using the easy interface of the web-server. Thank you in advance for any help you can provide.

-Kendy

2

See for example: Dealing with elemental ions

Is your case the residue name should be K1 and atom name K+1

Note that this forum is searchable.

3

I apologize for the redundant post. I did not realize I could search the forum, but thank you very much for your assistance.

-Kendy