From: M K (
Date: Wed Dec 03 2014 - 02:31:53 CST

Thank you for your help John.
My need may not be exactly related to psf files:

I'm facing some cases, in which I don't have the structure file in neither
pdb (because of more that 9999 residues) nor mol2 formats. I have built it
in Mat Studio.

I'm going to use VMD for simple analysis, like RMSD, Hydrogen Bonds
analysis and etc. Accordingly, I want to be able to select different
molecules and atom types easily. For example, I want to easily select the
polymer chain or deselect water molecules. Or, I want to select different
residues or atom types. *How can I have an intelligent pdb file (like those
in RCSB databse)* for my polymer water system to do md simulations in
software such as lammps and gromacs and visualize them in vmd?
For my structures, I have the xyz, res, car/mdf, cif, and lammps data (by
topotools) files.

What do you suggest to do?

On Wed, Oct 1, 2014 at 11:02 PM, John Stone <> wrote:

> 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
> 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
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> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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