restraints

From: Michael Grabe (mgrabe_at_itsa.ucsf.edu)
Date: Mon Dec 15 2003 - 20:04:29 CST

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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