Re: on NAMD simulation of DNA translocation through nanopores

From: Axel Kohlmeyer (
Date: Sun Jul 19 2009 - 11:24:06 CDT

On Sun, 2009-07-19 at 20:27 +0800, wrote:
> Hi,
> I am a newcomer in this field. Right now I am trying to simulate


newcomer to MD at all? newcomer to NAMD? or newcomer to the
kind of system that you want to do?

> 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.

1a) neutralize, solvate, equilibrate and test just this single
stranded DNA first (and use a not too long one for efficiency
reasons). before undertaking any larger calculations of compound
materials, you should first make sure that you know how to handle
the individual components well.

> 2) prepare coordinate file of gold nanopore under Materials studio
> GUI, and save it as a pdb file.

don't even consider to go here or further, until you are done with 1a).
if you move on, you'll be putting yourself into a lot of trouble, as
your project seems very ambitious.


> 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

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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