RE: AMBER: isolated NTP

From: Steve Seibold <seibold.chemistry.msu.edu>
Date: Mon, 18 Jun 2007 08:20:21 -0400

Hi Dave

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.

 

Thanks,Steve

 

-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of David A. Case
Sent: Monday, June 18, 2007 1:40 AM
To: amber.scripps.edu
Subject: Re: AMBER: isolated NTP

 

On Fri, Jun 15, 2007, Steve Seibold wrote:

>

> I am trying to make a single isolated NTP in nucgen using DAN, but

> the output tells me that DAN is an "unknown residue".

  ^^^^^^^^^^

 

What output (*exactly*)? If you load any of the standard leaprc files,

and type "list", you will see that DAN is available. So, we need to
know

what you really did to get the "unknown residue" reply.

 

...dac

 

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Received on Wed Jun 20 2007 - 06:07:19 PDT
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