AMBER Archive (2003)

Subject: Re: AMBER: distrance restraints for alpha carbons

From: David A. Case (case_at_scripps.edu)
Date: Mon Nov 03 2003 - 17:06:57 CST

On Mon, Nov 03, 2003, Sheldon Holder wrote:
>
> 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....
>
> I get the following error messgae:
>
> ERROR no map function for CA GLU :data= 1 GLU CA 20 GLU CA
> 13.52 13.52

In order to help prevent typographical errors in restraint files, the "map"
files are limited to common NMR-types of restraints, and atoms are not mapped
to "themselves" by default; that is, every atom listed in the input to
makeDIST_RST must explicity appear in the map file you use. As noted in
an earlier e-mail, some files do have atoms mapped to "themselves", and these
are probably easier to use for your problem.

In every case, you should check at least some of the output restraints, to
make sure that they match what you really want, i.e. that makeDIST_RST has
done what it should have done.

..dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu