AMBER Archive (2008)

Subject: Re: AMBER: NMR refinement

From: David A. Case (case_at_scripps.edu)
Date: Mon Jun 30 2008 - 09:44:51 CDT

On Mon, Jun 30, 2008, teresa.ierano_at_unina.it wrote:

> I have problem with NMR refinement.
> I read and followed the tutorial for Amber refinement of a DNA duplex
> and it works but I when I apply the same instructions to my
> oligosaccharide molecule it gives a message of error saying that it
> doesn't recognise my fragments.

> Then I tried to modify the file MAP (map.DG-AMBER called by default by
> typing makeDIST_RIST)in order to insert in it my fragments by it
> doesn't work again saying this time that it doesn't found the "NOE
> pathway".

I think we will need detailed information on *how* you modified the
map.DG-AMBER file. We would also need information on what program you were
running, with what inputs and flags, when you received the "NOE pathway" error
message. Also, please give the exact error message (I don't recognize it,
and the phrase "pathway" doesn't seem to be in either sander or makeDIST_RST.)

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu