Add bonds and topology file problem

From: Edroaldo Lummertz da Rocha (
Date: Sun May 01 2011 - 15:20:01 CDT

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
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?

Edroaldo Lummertz da Rocha

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