Re: Simulation with denaturants?

From: Peter Freddolino (
Date: Sat Apr 29 2006 - 16:11:16 CDT

Hi Patrick,
you can also do this in VMD by slightly tweaking the autoionize script
that comes with it. If you add your denaturant in the place of, say,
sodium, and add in a little section to randomly rotate each molecule
(which shouldn't be too difficult) this should work fine for placing a
chosen concentration of either of your denaturants (if you're using
GuHCl, it'll be analogous to placing NaCl; for urea treat it like a
single ion). The high ionic strength shouldn't be a problem in principle
so long as there are reliable parameters and the net system is neutral
(and it sounds like both of those guidelines are followed here).


Joshua D. Moore wrote:

>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?
>>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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