Add bonds and topology file problem

From: Edroaldo Lummertz da Rocha (edroaldo_at_gmail.com)
Date: Sun May 01 2011 - 16:57:16 CDT

2011/5/1 Axel Kohlmeyer <akohlmey_at_gmail.com>

> On Sun, May 1, 2011 at 4:20 PM, Edroaldo Lummertz da Rocha
> <edroaldo_at_gmail.com> wrote:
> > Hi NAMD users, when I add bonds between atoms in my model with topotools
> > plugin and save the .psf file, the atom types is replaced by atom names
> and
>
> can you please produce a script or sequence of commands that you
> execute that demonstrates that? topotools is not supposed to and to the
> best of my knowledge does not change any atom types unless you explicitly
> ask for it.
>
> > when I do a molecular dynamics I got an error related to that. For
> example,
> > in my parameter file I have the atom type AU for gold and in my topology
> > file I have atom names as A1, A2, An. I have a psf file fo my all system
> > where I have the atom names and atom types as I said before but when I
> add
> > bonds in Tk console and save using "animate write psf test.psf" , the
> atom
> > types in the .psf file are replaced by the atom names I got an error to
> > execute a molecular dynamics. Does anybody have a suggestion?
>
> the only explanation that would be consistent with that behavior would be
> that you load a .pdb file and not the corresponding .psf file and then save
> a .psf from it.
>

That's it, a beginner mistake, sorry. Thanks very much for your time. Now
everything is OK.

>
> axel.
>
>
> > --
> > Edroaldo Lummertz da Rocha
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>

-- 
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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:03 CST