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As the title says. How can I do it in OpenVAS? The other group has a website for example: https://thiswebsite.com/main.php and in that website there is a web application for example: https://thiswebsite.com/application/register.asp

Both sites are hosted in the same server. I don't know if scanning the IP address of the server will be enough to know the vulnerability also of the web application. Upon trying we only get results containing php vulnerabilities.

also, is there a tool where we can see what OpenVAS is doing during the scan? Something like, you can see what port the tool is scanning currently, how much load/traffic is being thrown on the target.

Thanks.

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OpenVAS is not an application scanner. It is a vulnerability scanner. It is worth reading Greenbone's documentation on it here.

If your web application has a vulnerability that OpenVAS has in its database, and you scan the IP address and port that the web app is on, then yes, it should be found.

Greenbone also gives you the progress of scans by IP (but not by port, as far as I can remember)

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    While the above is absolutely correct there are some basic SQL, Directory Traversal and Command Injection tests available which you can enable via the "Enable generic web application scanning" of the "Global variable settings" NVT preferences. Additionally if this is a known web application and a vulnerability tests exists it will be checked for this vuln by default. Furthermore you can include additional web app scanners like w3af or Acunetix via the OSPd wrapper listed at openvas.org/install-source.html – cfischer Jun 28 '18 at 19:18

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