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The fixed Percentage or Amount will be deducted at the time of vendor payment and posted to defined chart of accounts
1. Option to be provided to the users for defining percentage or amount2. System should calculate the deduction amount based on the percentage input and the "Debit" Line amount3. Deducted amount should be posted according to the GL Mapping
Accounts Payable > Payment > Payment Journal
Looks like you are talking about TDS. If yes then TDS functionality of Indian Localization can be used else you need to customize.
In reply to Sandeep:
Did you ever find a solution to this problem? If yes, would you mind sharing it with us?