Disclaimer:
I don't have vnc installed so guessing a bit here.
"xrdb" shouldn't be pointing anywhere unless you want to change some default settings by using .Xresources which clearly isn't found in $HOME.
If you want to know what your current settings are, use:
"xrdb -query -all"
Not sure where that xrdb load command is in your setup but I suspect you used this blog post:
That uses/expects Xfce Desktop.
So either try
- removing or commenting out the xrdb line in your ~/.vnc/startup (you might not need it)
or
- create the wanted file and fill it with the "xrdb -query -all" output (or any changes you specifically want)
Good luck and do tell us how you go. 
