VMD-L Mailing List

From: Richard Wood (Richard.Wood_at_purduecal.edu)
Date: Thu Oct 02 2014 - 13:03:28 CDT

You should run your small molecule that is unparameterized through the SwissParam web site. Convert it to a mol2 file first.

Richard
________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Zeinab Emami [zemami_at_ku.edu.tr]
Sent: Thursday, October 02, 2014 11:45 AM
To: Mayne, Christopher G
Cc: vmd-l_at_ks.uiuc.edu
Subject: Fwd: vmd-l: making psf files

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<mailto: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<mailto: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 

--
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University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349<tel:217-244-3349>
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