Re: Gold nanoparticle and 1-octanethiol

From: Edroaldo Lummertz da Rocha (edroaldo_at_gmail.com)
Date: Thu Apr 28 2011 - 19:07:44 CDT

Problem solved. Thanks.

2011/4/27 Edroaldo Lummertz da Rocha <edroaldo_at_gmail.com>

> 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 <edroaldo_at_gmail.com>
>
>> 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 Ciência e Engenharia de Materiais
> GruDE - EEL - CTC - UFSC
> Phn. ----
> http://www.grude.ufsc.br
> Mude Sua Vida, Mude o Mundo
>

-- 
Edroaldo Lummertz da Rocha
Doutorando em Ciência e Engenharia de Materiais
GruDE - EEL - CTC - UFSC
Phn. ----
http://www.grude.ufsc.br
Mude Sua Vida, Mude o Mundo

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