VMD-L Mailing List

From: sarah k (dailycolors_at_gmail.com)
Date: Fri Nov 13 2009 - 23:59:28 CST

Hi dears,

I tried the automatic psf builder. I received an error saying that there is
an unparameterized component. Unfortunately, the program itself breaks the
molecule down. That's why when I'm done with paratool I face an error:
cannot read the topology file, MOLECULE DESTROYED BY FATAL ERROR.

I've checked and over checked every thing. There must be something wrong
with my parent molecule. It's the very _autopsf_tmfile.psf file, vmd has
created. In the file there was only 3 atom of the residue. I tried deleting
the information of the 3 atoms in the *.psf file to rewrite the required
data. It didn't work.

The tutorials contained nothing about the format of parent molecule. Should
it be a *.psf file? Do you have any suggestions? Thanks.

Enjoy life,

Sarah