How would you calculate cost of equity capital in case of a company running at loss ?

Using CAPM...another "fair" and simple one is the levered beta approach in a proforma framework--i.e., as a company is expected to raise more debt to finance its excess CAPEX, NWCsp, or NOL, Debt/Equity increases and beta can be adjusted for it. You certainly know about MM levered beta...well, using a little algebra, your expected levered beta increase is proportional to the Debt/Eq. increase (adjusted by1-Tax). A simple example: a company with a D/E of1 has losses over the next period which will be covered by doubling its debt (new D/E is2). If you assume no taxes will be paid, its new levered beta increases by50%--i.e., (2-1)/(1+1). It is very intuitive and fair.