Re: AMBER: isolated NTP

From: David A. Case <>
Date: Mon, 18 Jun 2007 08:39:06 -0700

On Mon, Jun 18, 2007, Steve Seibold wrote:
> I am attaching my input and output file. I would think that my input
> script is bad, but nucgen does not complain that no residue is present
> just it does not recognize it. Of course, I am basing my input script
> off of the online tutorial on DNA. To be honest, I cannot really
> understand the manual's description of how to build an input file. The
> online tutorial says nucgen can create "A single isolated adenine
> nucleotide is AN" and I am attempting to do just that, create a base,
> sugar with three phosphates.

OK, now I see. I should have picked up better the details of your original
post. Nucgen is not the path you want to take for this. Note that the the
contributed parameters page (off the Amber web site) has files for ATP and
GTP, so it is probably better to start there. It's possible that nucgen
could be patched to do what you want, but it really is pretty much limited
to created duplex DNA or RNA, and is so ancient that I doubt anyone will try.

...hope this helps...dac

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Received on Wed Jun 20 2007 - 06:07:23 PDT
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