Re: applying experimental constraints to a MD simulation

From: Luca Muccioli (
Date: Mon Mar 12 2007 - 02:45:29 CDT


  if you have a distribution of distances, to reproduce it your need of
course a number of protein structures. In my opinion, the best way of
deriving the models that you want would be to simulate the protein in the
experimental conditions (i.e. with the proper solvent), but maybe you are
looking for a cheaper solution. Your idea of restricting the
conformational space with costraints is good, both for equilibrating in a
solvent or in vacuum.
If you want to use only as an equilbration tool, you choose a big force
constant and than you free the system, otherwise you may choose a
harmonic potential that allows for the whole range of your distribution
to be thermally accessible in the simulation, and use directly the

hope that helps



Luca Muccioli, Ph. D.
Dipartimento di Chimica Fisica e Inorganica
Universita` di Bologna
Via Risorgimento 4
40136 Bologna (Italia)

Phone: +39-051-6446992
Fax: +39-051-2093690

On Mon, 12 Mar 2007, L. Michel Espinoza-Fonseca wrote:

> 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 <>:
> > 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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