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I want to create a second copy of my primary DNS. As it was hosted on GoDaddy it went down with others. I want to host a copy on my server as a backup. I do not want a auto sync and will keep it manually sync as its a very very small number of entries which change rarely.

How can I achieve it (assuming it can be done)?

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That may not help. We have our own DNS servers and when went down (like godaddy recently) it did not help us, as users to get to your DNS servers they have to get IP addresses of your servers from your register and your register is down :(. – Serhiy Sep 11 '12 at 21:11
@Serhiy It doesn't have to be that way. The TLD servers should know about the "glue" for your domain which will tell resolvers the IP addresses of your name servers when they ask for the NS records for your domain. The situation you describe indicates that there is no glue for your backup nameservers. – Ladadadada Sep 12 '12 at 6:34
@Ladadadada Well, our domain was not resolvable 2 or 3 times over last 2 years when went down and we have our own DNS servers. However, we keep our own DNS servers because we add/change A-records frequently, not for reliability. :) – Serhiy Sep 12 '12 at 16:29

Just configure 2 nameservers with the same configuration and for each zone served by these servers assigned 2 NSes from which one will point to the first nameserver and the other to the second one. Once this is done and working(to check it you can use the next link which describes how to do it How to test new nameserver before to make it live) you need to switch the NSes to these two at your registrar.

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