VMD-L Mailing List

From: Schreiner Eduard (eschrein_at_ks.uiuc.edu)
Date: Thu Dec 03 2009 - 23:01:58 CST

if you're using the autoPSF plugin, then yes.

On Dec 3, 2009, at 9:56 PM, Jim Parker wrote:

> 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.

The residue names your pdb file has correspond to AMBER
topology.

> I assumed that I didn't have the right topology file.

correct

> 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?
>

yes. Note that atom names may be different too. I think, the names for
the heavy atoms
are same in AMBER and CHARMM, but the names of the hydrogen atoms are
different.
You could rename the corresponding residues, write a pdb file without
hydrogens,
and use autoPSF to add them back.

Also, check the following answer on namd-l:

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/10853.html

> Any help resolving these topology errors would be appreciated.
>
> Cheers,
> --Jim Parker
> UTSA Physics and Astronomy
>
>

eddi

=====================================================
Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078
http://www.ks.uiuc.edu/~eschrein/
=============================================