distance constraint [Was: Re: AMBER: Steered MD & Jarzynski's equality]

From: Gustavo Seabra <gustavo.seabra.gmail.com>
Date: Thu, 03 May 2007 07:53:33 -0400

wang wrote:
> Dear all ,
> I want to use distance constraint ( Ca atom of 121th residue and Ca of
> 251th residue ) .
> Could you tell me how to do that ? I tried NOE module . But I still
> didn't success .
> thank you
> Wang

Hi Wang,

If all you want is to restrain a distance, you can use the 'nmropt=1'
and specifying the &wt section, as for example:

     &wt type=DUMPFREQ, istep1=1, /
     &wt type=END, /

Then, In the 'dist.RST' file, you can use something like:

     &rst iat=2,4, r1=3.98, r2=4.00, r3=4.00, r4=4.02, rk2=500.0 rk3=500.0/

to specify a distance restraint between 2 atoms. (In this example, I'm
fixing atoms 2 and 4 at 4.0 angstroms.) You can find more details in the
manual. Look into sections "5.8. Weight change information.", "5.9. File
redirection commands" and "6.12.1. Distance, angle and torsional
restraints" for more information.

P.S.: It would be best if you started a new thread, by creating a new
message to the address that appears in the bottom of the e-mail, and
writing a good, descriptive subject line, because some better qualified
people to give you advice may not be interested in the current thread
and may completely miss your message.

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Received on Sun May 06 2007 - 06:07:17 PDT
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