AMBER Archive (2003)

Subject: AMBER: distrance restraints for alpha carbons

From: Sheldon Holder (sholder05m_at_som.llu.edu)
Date: Mon Nov 03 2003 - 13:27:48 CST

I am using Amber 7 on an SGI Octane2 (IRIX) with the following specs:

Octane 2 running IRIX 6.5.18m
2 400 MHz MIPS R12000(IP30) Processors with MIPS R12010 FPUs
512 MB memory
V6 graphics
MIPSpro Compilers, version 7.4 (C++, C, f77, f90)

  I want to perform molecular dynamics on a peptide fragment. I am trying
to prepare distance restraints for use in Sander. I want to define the
distance retraints for alpha carbons. My 8 coloumn input file for
makeDIST_RST is shown below: (file name slh3064c8col.dist)

1 GLU CA 20 GLU CA 13.52 13.52
1 GLU CA 21 VAL CA 14.06 14.06
1 GLU CA 22 VAL CA 17.36 17.36
1 GLU CA 23 LEU CA 18.60 18.60
1 GLU CA 24 LEU CA 17.82 17.82
1 GLU CA 25 LYS CA 19.73 19.73
1 GLU CA 26 LYS CA 22.75 22.75
2 LYS CA 20 GLU CA 13.41 13.41
2 LYS CA 21 VAL CA 13.77 13.77
2 LYS CA 22 VAL CA 16.55 16.55
2 LYS CA 23 LEU CA 18.36 18.36
2 LYS CA 24 LEU CA 18.18 18.18
2 LYS CA 25 LYS CA 19.66 19.66
2 LYS CA 26 LYS CA 22.59 22.59

When I run make2DIST_RST using this input:

makeDIST_RST -ual slh3064c8col.dist -pdb slh3064b.pdb -map
$AMBERHOME/src/nmr_aux/prepare_input/map.DG-AMBER -rst slh3064c.dist

I get the following error messgae:

ERROR no map function for CA GLU :data= 1 GLU CA 20 GLU CA
13.52 13.52

Checking the map.DG-AMBER file I notice that the file has no parameters for
mapping alpha carbons. How can I prepare a distance restraint file for use
in Sander where the restraints that I want to specify are between alpha
carbons? Is there a different map file that I should reference?

-Sheldon Holder
Department of Microbiology
Loma Linda University
Loma Linda, CA 92350
sholder05_at_som.llu.edu

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