VMD-L Mailing List
From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Wed Oct 01 2014 - 09:51:19 CDT
If you have the mol2 and/or VMD's automated bond detection is correct, you can use the TopoTools plugin (https://sites.google.com/site/akohlmey/software/topotools) all of the bonded elements found in a PSF (e.g., bonds, angles, dihedrals). TopoTools has a function for guessing impropers, but it is better to set those manually where required. I frequently use this technique to construct PSF files for small molecule ligands from PDB files. If not included in your input, you will also need to manually set the atom types and partial charges using VMD's atom selection language.
On Oct 1, 2014, at 8:02 AM, John Stone wrote:
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.
On Wed, Oct 01, 2014 at 10:53:14PM +1000, M Karim wrote:
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
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/