Hi,
If you download the file, it shows you the format that is needed for
the 'makeDIST_RST'
script to work, and you can use this downloaded file to complete the
tutorial as written.
For NMR NOE distance restraints, you will need to provide the residue
number, name, atom name for each atom in the distance restraint, and then
the value of the upper NOE bounds, as detailed in the tutorial.
This data you will need to provide or gather yourself and manipulate using
whatever scripting you are comfortable with. You can look at BMRB for PDB
entries to see if there is more than one NMR NOE data format.
Hope this helps,
Christina
On Fri, Mar 1, 2019 at 9:34 AM RITUPARNA ROY <ritup176122023.iitg.ac.in>
wrote:
> Dear all,
>
>
> I am following this tutorial
>
> http://ambermd.org/tutorials/advanced/tutorial4/index.htm
>
> AMBER Refinement of a DNA Duplex<
> http://ambermd.org/tutorials/advanced/tutorial4/index.htm>
> ambermd.org
> AMBER ADVANCED WORKSHOP. TUTORIAL 4. AMBER Refinement of a DNA Duplex
> [created by Vickie Tsui; updated by Rhonda Torres. ] There is no single
> recipe to the "best NMR refinement."
>
>
> I am not sure how to create the 7col.dist in the Distance-restraints and
> 5col.bb and 5col.sugar in Angle restraints. Kindly help.
>
>
>
> Rituparna Roy,
>
> Junior Research Fellow,
>
> Department of Chemistry,
>
> Indian Institute of Technology Guwahati.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-----------------------------------------------------------------
Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
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Received on Fri Mar 01 2019 - 07:00:02 PST
