From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Dec 16 2003 - 22:19:08 CST
Hi,
This is an old feature that predates NAMD's Tcl scripting. These
restraints are only active when conformational free energy is active.
You can emulate this with a pmf { task = stop ... } block.
As an alternative, you can implement these restraints using TclForces.
-Jim
On Mon, 15 Dec 2003, Michael Grabe wrote:
> Dear group,
>
> I am trying to use atom-atom restraints to pull
> two groups together. I want to do this outside
> of a pmf run, but namd doesn't seem to be
> recognizing my input (i.e. the atoms don't
> get any closer no matter how large I make
> the spring constant)
>
> My input looks like this:
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> # distance restraints
> urestraint {
> dist (S1, 56, cd) (S1, 66, cz) kf=10 ref=3.0
> dist (S2,157, cd) (S2,167, cz) kf=10 ref=3.0
> dist (S3,258, cd) (S3,268, cz) kf=10 ref=3.0
> dist (S4,359, cd) (S4,369, cz) kf=10 ref=3.0
> }
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Is there something wrong with this? This piece of the script
> comes near the end of the file. Does that matter?
>
> Any help is welcome.
>
> -Michael
> ------------------------------------------------------------------------
> --------------------------
> Michael Grabe, Ph.D.
> Post-doctoral Fellow
> Howard Hughes Medical Institute
> University of California, San Francisco
> 533 Parnassus Ave.
> San Francisco, CA 94143
> mgrabe_at_itsa.ucsf.edu
> tel: ++ 415.476.6585
> http://itsa.ucsf.edu/~mgrabe
>
>
>
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