how to calculate SIFT/SURF descriptor for 1 point?

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I only know x,y coordinate, how can I choose other parameters?

It depends on what you want to do. You can set fixed values for every point but you will loose rotation/scale invariance.

I want to input point descriptor to SVM to classify points.

And why do you need self-defined keypoints?

for example I put point at eye location and train SVM to detect eyes.

So you have to mark the points manually. You could mark a circle, then you would have a size for your feature. And set the angle to 0. But if you want do detect eyes in a picture, this will only work, if some keypoint detector detects a point with the same size and angle.

I know that sometimes people use different detector and descriptor(for axample Harris for corner detection+SIFT for descriptor extraction), isn't it points that detector and descriptor extractor are independent?

Yes, you can use any combination of detectors and descriptors. But using different detectors will generally yield different keypoints and thus different descriptors. If you detect features with MSER, you won't get the same keypoints (with the same size/angle) as you marked manually.