Problem with A string
 

He a string on my bass seems to be sitting too high in the nut if the bass, and when I play an open A it makes a "clunk" type of sound. Any suggestions to fix the problem.

classic fender bass problem, no angle on the A string over the nut;

use extra wraps on the A string, making sure they wind all the way to the bottom of the tuner post.

Well I've already put my strings on, so is there a way to fix it with the strings on the bass?

You can loosen the string a bit, push the wraps down as much as you can and bring it back to pitch. This may help. Short of installing a longer A string (or adding a second string tree, which has its own issues), the only other solution I've used is a twist tie over the E and A strings to dampen the vibration of the A past the nut.

BTW, this is not an issue with the nut, so do not alter the nut. The string is not "sitting too high" in the nut, it simply has insufficient break angle to dampen the vibration.

Question: Is the string sitting in the nut groove, or actually sitting on top of the groove?

I have mentioned in past posts, if the A string has been cut too short to wind to the bottom of the post, and the post is of the beveled type, a plastic zip tie pulled tight around the middle of the bevel lets you start your windings at the mid point of the post and wind further down increaesing the break angle ... a band aid fix at best, but if the string is already cut, not much other choice ... clip the zip tie short and you dont even really notice it ...

It's my opinion that the OP believes that the string is too high in the nut slot because the non-active portion of the string is higher behind the nut than the other strings. If the string were sitting too high, it would actually increase the break angle and potentially reduce the offending vibration.

I like tjh's idea of a zip tie on the tuning post. Cleaner than my idea of a twist tie on the streings themselves.

It's sitting in the nut, so like previously said it's not the nut

When I hit an open A the string vibrates in the nut, but it doesn't come out of the nut

Then go with the good advice, above.