Re: on NAMD simulation of DNA translocation through nanopores

From: Eduardo Cruz-Chu (
Date: Sun Jul 19 2009 - 15:21:19 CDT

VMD now has an inorganic builder, which started from the nanopore
project in the group.

If you want to create your gold nanopore system, just use VMD
(Extensions>Modeling>Inorganic Builder). Unfortunately there is no
tutorial yet, so you have to figure out how it works by clicking all
buttons until you get what you want. The task are very intuitive
though. That will take care of your steps 1 and 2.

Then, for the gold parameter file, I guess UFF is a good starting
point, I never tried though. You can also take a look at this paper about
Gold-binding proteins:

Rosemary Braun, Mehmet Sarikaya, and Klaus Schulten. Genetically
engineered gold-binding polypeptides: Structure prediction and molecular
dynamics. Journal of Biomaterials Science, 13:747-758, 2002.

On Sun, 19 Jul 2009, wrote:

> Hi,
> I am a newcomer in this field. Right now I am trying to simulate the
> translocation of single-strand DNA through a gold nanopore under applied
> electrical fields.
> Below is the procedure I scheduled. Can you please have a look and make
> comments?
> 1) prepare DNA coordinate file (pdb) with NAMOT.
> 2) prepare coordinate file of gold nanopore under Materials studio GUI, and
> save it as a pdb file.
> 3) merge DNA pdb and gold nanopore pdb into one.
> 4) modify CHARMM topology file and parameter file to include description of
> gold nanopore, interaction between Au and other atoms (based on UFF model).
> 5) generate psf file of the system with its pdb file and modified CHARMM
> topology file.
> 6) immerge the system into water sphere.
> 7) do minimization and equilibration.
> 8) set fixed atoms, and forces on DNA atoms according to their partial
> charge.
> 9) do steered MD simluation
> My first question is that at step 2) is there any easier method to pdb file
> of prepare gold nanopore? Since I have to change the diameter and
> conformation of gold nanopore many times to find the best fit size, I don't
> hope to write it by hand every time I make some changes.
> My second question is that at step 4), should I describe every Au atom in
> the gold nanopore as one residue in topology file, or just describe a
> supercell of gold crystal?
> Any suggestions are greatly appreciated!
> Yuhui

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