Hi
With holding tax should be calculated automatically. Have you defined a percentage in the with holding tax code used for payment? Refer the blog below
http://scn.sap.com/docs/DOC-48399
Also check the field status of the GL Account should have the below fields at least as optional:
1. With Holding Tax Code
2. With Holding Tax Amount
3. EC Tax Code
regards
Sanil Bhandari