VMD-L Mailing List

From: Jim Parker (jim.parker_at_prismsciences.com)
Date: Thu Dec 03 2009 - 21:56:00 CST

Hello,
  I am attempting to use autoPSF to generate a .psf file to associate
with a .pdb for a DNA segment I want to analyze. The GUI based program
that comes with vmd seems to be straight forward

1. Choose the .pdb file
2. Select topology files
3. Select an chain
4. Generate .psf

When I attempt the above, I get an error "AutoPSF detected 32
unparametrized components"
and it lists the base pair names DT, DG, DA, and DC.

I assumed that I didn't have the right topology file. So I found this
list of CHARMM topology files
http://www.ccl.net/chemistry/resources/messages/2001/11/29.006-dir/index.html

which indicated to me I just need to include a file like

    (4) top_all27_na.rtf all hydrogen RTF for nucleic acids

but, didn't work. I added every *.rtf that had _na_ in the name. Still
didn't work.
looking at the *_na.rtf files they define residues as GUA, ADE, CYT, and
THY -- Do I have to rename each section prior to using AutoPSF?

Any help resolving these topology errors would be appreciated.

Cheers,
--Jim Parker
UTSA Physics and Astronomy