If I can get an average profit of 0.5% per trade, and there is a commision of 0.005 per share, can it ever be profitable to trade penny stocks(1$ to 6$)?
Are you asking if you aim for a profit of 0.5% profit on each trade if you can be profitable? That means for every $1000 of capital you trade you only expect to make $5 in profits.
Even if you could achieve a 95% success rate, one or two losses would wipe you out.
Successful trades achieve their profitable results by letting their profits run and taking small losses early. Most successful traders only achieve around a 50% success rate, but have average profit size at least 2x to 3x their average loss size.
So no, I don't think you will be successful and profitable trying to make many small profits, nor by trying to trade penny stock (which by definition are less than $1).
Small correction: Your title asks about trading $1 to $3 stocks but the body talks about trading $1 to $6 stocks. It doesn't really matter mathematically since both upper limits are above the threshold for gain.
Given the percent gain and the commission fee that you provided, you must trade stocks that cost more than $2 in order to make a profit. Otherwise, it's a guaranteed loss, no matter how many shares you trade because the commission will exceed the profit. The one exception to this would be 100 shares at $2.01 which would yield no gain.