VMD-L Mailing List

From: Jim Parker (jim.parker_at_prismsciences.com)
Date: Fri Dec 04 2009 - 22:13:50 CST

eddi,
  Thanks!! The script from the namd-l archive did the trick.

Cheers,
--Jim Parker

Schreiner Eduard wrote:
> 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/
> =============================================
>