Gold nanoparticle and 1-octanethiol

From: Edroaldo Lummertz da Rocha (
Date: Mon Apr 25 2011 - 13:14:22 CDT

Dear NAMD users, I am starting to build a topology for molecular dynamics
simulations and I am facing some problems. My system consists in a trunctaed
octahedron gold nanoparticle and I want to put a 1-octanethiol monolayer on
the nanoparticle surface. I write a script to generate the psf to
nanoparticle but I do not have bond information. I also build the topology
for 1-octanethiol by hand and generate the psf using psfgen. My problem is
combine these two systems in order I have the 1-octanethiol on the
nanoparticle surface. I used the script provided in the Bionanotechnology
tutorial to combine (combine.tcl) the two systems but I get the follow
message error when I run the script in the VMD TkConsole:

clearing structure, preserving topology and aliases
reading structure from psf file gold.psf
Error processing bonds

MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

So, I do not have bond information in my nanoparticle and my question is: Is
this information really necessary? Is there anyway to build my
nanoparticle-1-octanethiol system topology? Do I need to write a script for
that? Do you know a way to do that? That's it, Thanks very much for your
time and suggestions.

Edroaldo Lummertz da Rocha

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