( protein )
3 December 07
in protein

Poking my eyes out with Amber, again

So I’m trying to work out how to create topology files for non-protein ligands, and I come across the .OFF file, which stores parameters for certain ligands. I google the .OFF format and come across this query in the AMBER mailing list:

Where can one obtain a description of the .OFF file
format? Many thanks, Jan Rosenzweig

To which, we got this reply:

It has never been documented. Reading the code is the
only way; however, it is not hard to figure out once
one gets started. Bill Ross

Holy fuck me jesus – is this really the answer – reading the code to get a description of the file format?

Neil on 12/03 said:

Amazing, isn’t it. But the answer is yes, in many cases. I can just about understand it if you release code/software that you think almost nobody will use, but AMBER is pretty well known and used widely?

Egon Willighagen on 12/04 said:

Quite common for QM software indeed. Moreover, the format tends to change bit-by-bit going from one version to another, or even from one operating system to another. This makes parsers tricky… but there are plenty of tools around to do that. Have a look at:

http://www.redbrick.dcu.ie/~noel/OpenSource.html

Bob on 12/13 said:

Amber developers do charge users ~$400 for license. If I remember correctly, this Bill Ross is a developer.