Hello, I think program can't be so accurate only with flow rate and column info the parameter which also have a influence on RT is system is dead volume which you should have for prediction.
I think, that more useful is to find a program that will calculate hydrophobicity of molecules of your interest. You probably need just only order of elution of individual compounds from your mixture. Precise estimation of RT depends on many factors and usually is not so important. You can try ACD ChemSketch, where the feature is free for one month after installation.
I hope all is well! I don't have a full answer for you but rather a tip who to contact with your question. I know dr Leon Barron from KCL has worked on comprehensive models for LC retention time prediction. Maybe he can help you!
I am noting this question way too late. Our group has been developing a LC retention prediction software tool that uses data from real chromatograms to predict retention times under "any" mobile-phase composition method. It can also be used to extrapolate retention parameters from your specific molecules.
We do not have it publically available yet, but I can share with you an alpha version.