VMD-L Mailing List

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Sat Nov 14 2009 - 07:47:23 CST

Hi Sarah,

What are the problematic atoms that AutoPSF is complaining about? Sometimes AutoPSF does a poor job of assigning chain values, especially if your initial PDB file has residue names that can't be found in the topology file. Where did you get the original PDB file?

Josh

On Nov 14, 2009, at 12:59 AM, sarah k wrote:

> 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
>