AMBER: Sander--NMR refinement

From: Esther Brugger <>
Date: Thu, 21 Dec 2006 20:39:48 -0800 (PST)

Dear Amber Users,
 I am using "distance restraints" do the the NMR refinement by Sander. I have some problem to generate the input file.
 I prepared the 8 column file first, here is some parts of it:
   1 MIC H118 1 MIC H129 2.00 5.00
   1 MIC H79 1 MIC H90 2.00 5.00
   1 MIC H40 1 MIC H51 2.00 5.00
   1 MIC H 1 MIC H11 2.00 5.00
   2 MIC H118 2 MIC H129 2.00 5.00
   2 MIC H79 2 MIC H90 2.00 5.00
   2 MIC H40 2 MIC H51 2.00 5.00
 But when I use makeDIST_RST to generate the input file, it shows some errors:
 ($AMBERHOME/exe/makeDIST_RST -ual 8col.dist -pdb Mol.pdb -rst RST.wc)
 # makeDIST_RST
 Currently configured for up to 5000 atoms
 Using MAP file /home/amber/amber8/dat/map.DG-AMBER
 ERROR no map function for H118 MIC :data= 1 MIC H118 1 MIC H129 2.00 5.00
 What does it mean? Do I need to change the residue name and atom name according to the file "map.DG-AMBER" in the "8col.dist" file? If so, it means I also need to change the resiude and atom name in my pdb file, right? But my molecule is not a standard protein. I really wish someone could help me to do it! Thanks a lot!
 Happy Holidays,

Esther B.

Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Dec 24 2006 - 06:07:30 PST
Custom Search