Ion.top file to submit my own PDB files


#1

Hello. I am submitting my own pdb files. The receptor hast two Cu+1 ions and I would like to be sure that the ion naming is consistent with the ion topologies provided in HADDOCK. I do not have the ion.top file to corroborate this info. May one of you send me this file to corroborate the information of these ions?

All the best,


#2

Check box 3 (or 4) of our Nature Protocols 2010 paper describing the server.

S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin
The HADDOCK web server for data-driven biomolecular docking.
Nature Protocols, 5, 883-897 (2010).
http://www.nature.com/nprot/journal/v5/n5/abs/nprot.2010.32.html

In short: the residue name should be CU1 and the atom name CU+1

Cheers
Alexandre