AMBER Archive (2006)

Subject: Re: AMBER: Sander--NMR refinement

From: David A. Case (case_at_scripps.edu)
Date: Tue Dec 26 2006 - 12:44:46 CST

On Thu, Dec 21, 2006, Esther Brugger wrote:
>
> 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

If you have constraints to a non-standard residue, it's usually easiest just
to enter them in the "raw" (&rst namelist) format. The makeDIST_RST program
is just a front-end to make this process easier for standard problems.

You could also modify the map.DG-AMBER file to include your MIC residue -- you
pretty much have to work by analogy to the existing residues, and/or read the
code. That's why this is not usually the recommended procedure.

...good luck...dac

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