AMBER Archive (2007)

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

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Thu May 03 2007 - 06:53:33 CDT

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, /
     DISANG=dist.RST
     DUMPAVE=restraint.log
     LISTIN=POUT
     LISTOUT=POUT

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.

Gustavo.
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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