input limit for screening libraries against a pharmacophore?

Hello,

I'm experiencing difficulties when attempting to screen a large subset of molecules against my pharmacophore of interest. I have an SD file with ~800,000 prepared molecules that I'd like to fit, however, when the program calls them up, it only seems to read ~20,000 before quitting. Is there a way aside from using smaller input files to circumvent this problem?

Cheers,

Paul