VMD-L Mailing List

From: Zeinab Emami (zemami_at_ku.edu.tr)
Date: Thu Oct 02 2014 - 11:45:27 CDT

Dear Christopher Mayne,

I have the same problem. I tried to follow you advise, though could not
figure out how it wors up to now. The tutorial seems not comprehensive.

I also read this page:
http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/ which did not help
much as well.

Would you please give me a short hint on *the procedure for producing PSF
file from a given pdb file that is void of parameter info.*

E.G. I tried to modify this pdb file for ethane, in order to get its psf
file:

HETATM 1 C 0 -0.772 0.000 -0.000
  C
HETATM 2 C 0 0.772 0.000 -0.000
  C
HETATM 3 H 0 1.179 1.012 -0.083
  H
HETATM 4 H 0 1.178 -0.578 -0.835
  H
HETATM 5 H 0 1.178 -0.434 0.918
  H
HETATM 6 H 0 -1.178 -0.432 0.919
  H
HETATM 7 H 0 -1.178 -0.580 -0.834
  H
HETATM 8 H 0 -1.179 1.012 -0.086
  H
END

I changed the atom names and type manually, and the charges as well, it did
not work.

I thank you in advance and look forward to hear your advise.

Sincerely,
Zeinab

On Wed, Oct 1, 2014 at 5:51 PM, Mayne, Christopher G <cmayne2_at_illinois.edu>
wrote:

> MK,
>
> 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.
>
> Regards,
> Christopher Mayne
>
> On Oct 1, 2014, at 8:02 AM, 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
> 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
> 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/
>
>
>