Hi Sarath,
If you want the particular Vendor to be paid always by a particular house bank, then update the Vendor master data (Field LFB1-HBKID) with this house bank.
If your requirement is to pay particular Invoices by a particular House Bank on case to case Basis, then enter the House bank in Vendor Invoice, so that Payment run can consider the same.
Hope that helps
BR
Amitash