A p-value of 0 means the value is really low or close enough to zero. MutSig always produce 0 pvalue for overly significant genes such as TP53 in solid tumors. If you really want some value instead of zero, replace them with lowest machine epsilon values.

In r you could do this by

mutsig = read.delim('sig_genes.txt', sep = '\t', stringsAsFactors = FALSE, header = TRUE)
mach.epsi = .Machine$double.eps
mutsig$q = ifelse(test = mutsig$q == 0, yes = mach.epsi, no = mutsig$q)