Withdraw on Transcript

Hi all, I am currently an undergraduate 3rd year student at civil engineering in Turkey. One of my future plans is to attend a graduate school for masters in civil engineering. As most of you know, the admissions for the grad schools are done in the end of the 3rd year. This semester, i am having trouble with one of my courses which I will probably end up getting a F or D. So I am thinking of withdrawing the course. I have a good GPA (3,83) and a F or D will lower my GPA significantly. So, do you guys think having a withdraw course on transcript will effect my chances for the adminssion to schools like UC Berkeley, Stanford etc or will it not be such a big deal? Thank you for your comments.