ADL: Parameters for docking with metal ions in receptor
I was concerned about using copper and sodium cations with autodock 4.
Since none of those are in the default ff file, I did a little search
in the internet. Finally I can give you this batch (see below). I`ve
tested it for Cu and Na and did not observe any severe errors.
The idea of this message is to
1/ Give starting parameters for those who want to run a docking
experiment from scratch
2/ Start a thread discussing this parameters. May be some of you have
something better that you would like to share. It shall also be
appreciated to discuss possible errors.
Re: ADL: Parameters for docking with metal ions in receptor
Hello, I'm not an expert on parameters, so don't know if what you've found
out works, but have to remind you -since I came across the same issue-
XCSCORE scoring function cannot distinguish different metals.