Is there a sin upon the questioner due to the strained relationship with his deceased father, who was not committed to some religious teachings and refused his advice, and can he atone for this sin?

If the situation is as you described, then you were dutiful towards your father, and there is no sin upon you for disobeying him in matters that contravene the Sacred Law. Obedience is only in what is good, and there is no obedience to a creature in disobedience to the Creator. As long as you treated him well and did not fall short in his rights, then his displeasure with you does not harm you. You can make up for honoring your parents after their death by supplicating and seeking forgiveness for them, giving charity on their behalf, maintaining ties of kinship through them, and honoring their friends.