Re: Gold nanoparticle and 1-octanethiol

From: Edroaldo Lummertz da Rocha (
Date: Wed Apr 27 2011 - 07:01:52 CDT

Dear NAMD users, I still do not have a suggestion to my answer. Is it very
basic? Sorry for this second e-mail but I need to solve this problem to
proceed. Thanks so much.

2011/4/25 Edroaldo Lummertz da Rocha <>

> 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

Edroaldo Lummertz da Rocha
Doutorando em CiÍncia e Engenharia de Materiais
Phn. ----
Mude Sua Vida, Mude o Mundo

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