Re: AMBER: for NMR restrains files

From: Prem Prakash Pathak <>
Date: Sat, 8 Sep 2007 10:06:11 +0530

Dear Wenyong,

>I wonder how I can conver to the " 7-column " file
>needed for input to makeDIST_RST.
I am pasting below lines from the tutorial from web page of amber, i
hope it would solve you problem.
1. Distance restraints

The program used to convert a 7-column file to the much less intuitive
AMBER restraint file is makeDIST_RST. Typing makeDIST_RST -help will
give directions on how to run the program. You will also need to
specify the template PDB file and the MAP file (this by default can be
found in $AMBERHOME/dat/map.DG-AMBER), which maps distance geometry
pseudostructure nomenclature onto all-atom nomenclature used in AMBER.

makeDIST_RST -upb 7col.dist -pdb gcg_b.amb.pdb -rst RST.dist

2. Torsion angle restraints

To make the torsion angle restraints, traints (

To convert the 5-column file into an AMBER-format restraint file, use
makeANG_RST. The usage of makeANG_RST is:

 $AMBERHOME/src/nmr_aux/prepare_input/tordef.lib. You could also
specify your own nomenclature or add extra angles by copying and
modifying this file. For this example, we will use the standard

makeANG_RST -pdb gcg_b.amb.pdb -con -lib
$AMBERHOME/src/nmr_aux/prepare_input/tordef.lib >


On 9/7/07, Wenyong Tong <> wrote:
> Hello Amber Users,
> I use the Sparky for the assignments of my sugar NOESY
> spectrum.
> I wonder how I can conver to the " 7-column " file
> needed for input to makeDIST_RST.
> Thanks in advance.
> Wenyong
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Received on Sun Sep 09 2007 - 06:07:41 PDT
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