From: sarah k (
Date: Sat Nov 21 2009 - 06:57:32 CST

Hello all,

I'm working on an organic compound. Its topology file wasn't available. So I
used QMtool and defined atom properties, autogenerated all coordinates and
wrote the Gaussian file. Then I saved the new pdb file as qm.pdb. After that
I used paratool. My parent molecule was my first .*pdb file and I chose my
created qm.pdb file as my base molecule. Then again I edited atom properties
just like before and then I autogenerated coordinates. Then I wrote the
topology and parameter files.

Before doing such things, autopsf builder would generate an error saying
molecule destroyed by fatal error. But now it does create the _autopsf.psf
and _autopsf .pdb files successfully. Actually my origin file is a complex
containing an organic compound plus a protein. The point is that when the
psf file is written successfully (as the program claims!) we see a perfect
molecule in the window. When I open the complex file or the autopsf.pdb file
of the compound, I see a destroyed molecule with just several atoms.

I've enclosed the *.pdb, *qm.pdb, *autopsf.pdb files of the compound and the
topology file created by paratool. (I should add that when I use the
complex, I add the topology file of the compound to the origin topology
file, top-proteinů.inp, and save the file in wordpad by the format of *.txt.
and then I use just the new txt file when running psf builder.)

I have to solve the problem even if I there be no way but programming a new
NAMD! Thanks in advance for your help and attention.

Enjoy life,


  • chemical/x-pdb attachment: 65.pdb
  • application/octet-stream attachment:
  • chemical/x-pdb attachment: 65.pdb