AMBER Archive (2005)

Subject: Re: AMBER: Formatting a restraint file

From: Furse, Kristina Elisabet (kristina.e.furse_at_vanderbilt.edu)
Date: Thu Apr 14 2005 - 15:02:20 CDT

They are DISTANCES if you're restraining a distance, angles if you're
restraining an angle, or torsions if you're restraining a torsion. All depends
on values of iat (p 119).
K

Quoting Kara Di Giorgio <kdigiorgio_at_sbcglobal.net>:

> I think you explained it. I guess the missing info was that they are
> DISTANCES. I wasn't sure what the numbers meant.
>
> Thanks,
>
> Kara Di Giorgio
>
> On Apr 14, 2005, at 9:13 AM, Carlos Simmerling wrote:
>
> > the top of page 121 is pretty clear-
> > r1/r2/r3/r4 define the function used for the
> > restraint. those values are the distances
> > where the restraint function changes.
> > you determine the values based on what
> > distance range you want to penalize.
> > r1 and r4 are less important unless you
> > expect that the violations may become
> > large and you need a linear penalty instead
> > of harmonic- this is probably most useful
> > with nmr structure refinement.
> > between r2 and r3 there is no penalty,
> > so that could be the fluctuations you want
> > to allow or perhaps the uncertainty in
> > experimental data that you are using for the
> > restraint. it's hard to give one way to determine
> > these values since the restraints are used for so
> > many different purposes.
> >
> >
> > Kara Di Giorgio wrote:
> >> I've read that. It gives a lot of info about, if r2>r1 then this is
> >> used, etc, but no info about the meaning of the values of r1 or r2.
> >> How do you choose the values? What do the actual values mean?
> >> Kara Di Giorgio
> >> On Apr 13, 2005, at 10:06 PM, Furse, Kristina Elisabet wrote:
> >>> Kara-
> >>>
> >>> Have you read p. 121 of the amber8 manual? It describes how r1
> >>> through r4
> >>> control the restraint potential.
> >>>
> >>> Kristina
> >>>
> >>>
> >>> Quoting Kara Di Giorgio <kdigiorgio_at_sbcglobal.net>:
> >>>
> >>>> I'm trying to set distance restraints between the Ca and the O's of
> >>>> the
> >>>> protein.
> >>>>
> >>>> Any help is greatly appreciated!
> >>>>
> >>>> Kara Di Giorgio
> >>>>
> >>>> On Apr 13, 2005, at 2:18 PM, Carlos Simmerling wrote:
> >>>>
> >>>>> do you want positional restraints? in that case you don't
> >>>>> need the disang file. that's for distance, angle or dihedral
> >>>>> restraints. tell us what you are trying to restrain and we can
> >>>>> point you to the right spot...
> >>>>> carlos
> >>>>>
> >>>>> Kara Wald wrote:
> >>>>>
> >>>>>> I'm trying to restrain a Ca within a protein for a dynamics
> >>>>>> simulation and am having trouble formatting the DISTANG file.
> >>>>>>
> >>>>>> I've looked at the sample files in the manual and read the
> >>>>>> section.
> >>>>>> What are r1 through r4? In the manual, there is a blank listed
> >>>>>> next
> >>>>>> to them and I've found references to "should be formatted like
> >>>>>> r1through r4" but no info about what they stand for/mean.
> >>>>>>
> >>>>>> Thanks,
> >>>>>>
> >>>>>> Kara Di Giorgio
> >>>>>>
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> >>>
> >>>
> >>> -----------------------------------------------------------------
> >>> Kristina E. Furse
> >>> Department of Chemistry
> >>> Center for Structural Biology
> >>> Vanderbilt University
> >>> Email: kristina.e.furse_at_Vanderbilt.Edu
> >>> ---------------------------------------------------------------------
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-----------------------------------------------------------------
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
Email: kristina.e.furse_at_Vanderbilt.Edu
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