AMBER Archive (2003)

Subject: Re: AMBER: FW: Residual dipolar couplings

From: David A. Case (case_at_scripps.edu)
Date: Fri Sep 26 2003 - 15:36:25 CDT

On Fri, Sep 26, 2003, McAteer, Kathleen wrote:
>
> > I have been trying to implement residual dipolar coupling restraints into
> > my AMBER 7 molecular dynamics calculations but I am not happy with the
> > resulting distance (55.8) and alignment penalties (216.47). I think I may
> > be implementing the rdcs incorrectly as I have been successful using them
> > in X-PLOR and had very small restraint violations.

I think one would need more information. First, though, take a structure you
got from xplor and make sure that the initial violations are indeed low
when implemented in Amber. Also, try some things with just distance
restraints....under circumtances I am assuming you have (since you seem to
be using explicit solvent simulations) the dipolar couplings will just serve
to make the structure a bit better, so you want to make sure other parts
are working OK before adding them.

> > simulated annealing protocol, 20 ps
> >
> > &cntrl
> > nstlim=20000, pencut=0.001, nmropt=2,
> > temp0 = 300.0, tempi = 300.0, tautp=1.0, ntpr=100, ntt=1, ntwx=100,
> > ipnlty=1, tausw=0.0, mxsub = 45, iscale=5,
> > scalm=300, ntc=1, vlimit=20.,
> > cut=9.0,
> > &end
> > &ewald
> > &end
> > 46.9278231 47.9662761 62.9613200 90.0000000 90.0000000 90.0000000
> > 50.0000000 50.0000000 65.0000000 4 0 0 0
> > 0.000004

Note that the above three lines are not needed in sander7, and in fact are
ignored (I think). Make sure that they don't have anything you need...such
lines should never be needed.

..good luck...dac 

-- 

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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
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