Re: applying experimental constraints to a MD simulation

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Sun Mar 11 2007 - 18:55:26 CDT

Actually the idea is similar, but we're not using NMR constraints -for
that purpose, crystallographers use XPLOR. We have from FRET and EPR
data that we want to include in our model. They are very few
distances, though, which makes the things easier, I guess.

2007/3/12, Mark Abraham <Mark.Abraham_at_anu.edu.au>:
> L. Michel Espinoza-Fonseca wrote:
> > Hi all,
> >
> > I was wondering if my specific problem can be solved with NAMD -I
> > really hope so. Right now, we have all this bunch of experimental data
> > (CA-CA distance distributions, to be more exact), and I'd like to use
> > them as "constraints" to build a 3-D model of a protein, using MD
> > simulations. I've used the harmonic constraints parameters included in
> > NAMD before, but usually you apply a force instead of a given
> > distribution of distances. Based on this, I'd like to know if any of
> > you have an idea on how to fit one (or multiple) distribution(s) of
> > distances (let's say, from 45 to 55 A) into the MD simulation. All
> > comments will be greatly appreciated!!!
>
> It sounds like you're wanting to build a structure from NMR constraints
> - why not use the software that has been designed for that task? I've no
> idea what NMR people use these days, though!
>
> Be aware, though, that satisfying all of your constraints simultaneously
> can lead to producing an unphysical structure... NOEs are derived from a
> population of structures, and if there is significant disorder, then not
> all members of the population are producing all of the NOEs all the time...
>
> Mark
>

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