How to recover all protein ses into refseq database
As with most things, there are multiple ways to do this. Here are two of them: 

Download from the NCBI Assembly portal


Go to https://www.ncbi.nlm.nih.gov/assembly/ and search for 'Viruses[Organism]'. For our purposes, I am going to restrict this search to Virus assemblies that are latest RefSeq and reference genomes. The query for this will be: "Viruses"[Organism] AND "latest refseq"[filter] AND "reference genome"[filter]. It will return 46 results. 
To download the protein FASTA sequences for all of these, click on the big blue Download Assemblies button, choose RefSeq as source and Protein FASTA as File Type. 
Click the Download button and a tarball with FASTA files - one for each assembly - will be created for you to download. You will then have to combine them all into a single file. 



Download using wget


Go to ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral and download the assembly_summary.txt file. This is a tab-delimited file with information about every RefSeq viral assembly located in that FTP path. Column 20 has the FTP path for the assembly which you can parse out and use wget to download the protein FASTA file for each assembly, followed by combining them into a single gzipped file as shown below:

## download the assembly_summary.txt file
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/assembly_summary.txt
## download the protein FASTA files
grep -v '^#' assembly_summary.txt \
    | cut -f20 \
    | while read -r url ; do wget $url/*_protein.faa.gz ; done
## combine all files into a single one
zcat *_protein.faa.gz | gzip &gt; all_viral_proteins.faa.gz