VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 01 2014 - 08:02:49 CDT

Hi,
  If you have a mol2 file with bond information, you may not
really even need a PSF file if you're just wanting to analyze it in VMD.
You don't say what it is that you want to analyze, so it's hard to make
any concrete statements about what you would be missing if you just
proceeded using the mol2 file. If you can be more specific about your
goals it would be easier to give further guidance.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 01, 2014 at 10:53:14PM +1000, M Karim wrote:
> Hi,
> I have a structure that doesn't have a psf file for it. It is not a
> biological material (Nucleic Acid or Protein, so I think Automatic psf
> builder does not work for it) I have the xyz, pdb, and mol2 as well as the
> trajectory files for it.
> How can we make the psf file for this structure to better analyze it in
> VMD?
>
> Thank you
> MK 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
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