AMBER Archive (2006)

Subject: AMBER: Sander--NMR refinement

From: Esther Brugger (esther_brugger_at_yahoo.com)
Date: Thu Dec 21 2006 - 22:39:48 CST

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.

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