Hi Manvendra,
The advanced tutorial you are referencing formats restraint files for use
in Amber from a 7, 8 or 5 column format file.
This was done (I think!) because there are lots of ways that NMR restraints
are deposited in the PDB or BMRB.
Xplor, star, diana are all types of NMR restraint file formats.
The tutorial is meant to take information and, using scripts Amber provides
(makeDIST_RST, etc.), create the restraint file Amber (sander, pmemd) can
read.
It is up to you to get the initial information into the correct 5 or 7
column format.
You can use bash or awk to format the 5 or 7 column files: what I do is
read the NMR restraint file I download from the PDB, look up the format
type so I know what the numbers in each column mean, and then copy that to
a new file.
For example,
awk '{print $2}' file.dat > newfile.dat
prints the second column from one file (file.dat) to a new file
(newfile.dat).
Read the headers/descriptions of each column closely, and good luck!
-Christina
On Mon, Jun 30, 2025 at 12:34 PM MANVENDRA SINGH via AMBER <
amber.ambermd.org> wrote:
> Dear Amber group,
> I have been going through the AMBER tutorials and am currently trying to
> apply distance and Watson-Crick (WC) restraints in my simulations. However,
> I noticed that the tutorials provide the input files directly (
> https://ambermd.org/tutorials/advanced/tutorial4/index.php).
>
> Could you please guide me on how to write the input files for applying
> distance and WC restraints properly? Any references or examples would also
> be greatly appreciated.
>
> Thank you for your time and help.
>
> Best regards,
> Manvendra Singh
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
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Received on Mon Jun 30 2025 - 11:00:02 PDT
