Re: Simulation with denaturants?

From: Joshua D. Moore (
Date: Sat Apr 29 2006 - 15:56:10 CDT


Vega ZZ allows one to solvate with anything.

You have to create a box of your solvent with a PDB FAT format which
requires manually adding charges for your force field, but think shouldn't
be difficult since you only have to do it with one molecule. This is
explained in the user manual. Then you should be able to add your 1 M
GuHCl by varying the solvation box size. Vega ZZ will write out your
combined psf and pdb files for you. You can do the same for urea.


On Sat, April 29, 2006 3:00 pm, patrick wintrode wrote:
> I'm planning to run MD simulations of a protein in the presence of 1M
> GuHCl (we've already mostly finished the simulations in water). I know
> that parameters for GuHCl exist, because I recall that the Karplus group
> published some unfolding simulations with it.
> I was wondering: does anyone know of a script for placing the denaturant
> molecules in the water box? Maybe a script for some similar problem that I
> could modify?
> Also, we can use Urea instead. Do you think that the high ionic strength
> resulting from 1M GuHCl will cause particular problems that would make
> Urea preferable?
> Thanks.
> Patrick L. Wintrode
> Assistant Professor
> Dept. of Physiology & Biophysics
> Case Western Reserve University
> Cleveland, Ohio 44106

Joshua D. Moore
Graduate Student
North Carolina State University
Department of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC 27695-7905
Phone: (919) 513-2051
Fax: (919) 513-2470

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