on NAMD simulation of DNA translocation through nanopores

From: yuhuihe_at_ime.pku.edu.cn
Date: Sun Jul 19 2009 - 07:27:55 CDT

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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