VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Oct 13 2014 - 09:11:08 CDT

Zeinab,

The PDB format doesn't define an atom type, so it stands to reason that you won't see any change in the PDB file. Also, VMD doesn't appear to write charges out to PDB. Both of these data are instead updated when writing out the PSF file.

Regards,
Christopher Mayne

On Oct 13, 2014, at 4:00 AM, Zeinab Emami wrote:

Dear Christopher Mayne,

First, I like to thank you again for your informative answer to my question about producing psf file when getting the error of "Need to have at least one atom in your selection!".

I tried your guideline and changed the names, types and charges of each atom in the pdb file. Though

- when I change every parameter [atom name, atom type, atom charge], NO CHANGE AT ALL is visible in the output pdb file but in the atom names.

- Although the atom names change, the problem resists and I get the same error when I use autopsf.

I really don't expect you to tell me the last answer. I tried to search for a solution but failed. If you guide me to a useful document about this I would be grateful.

Sincerely,
Zeinab

On Thu, Oct 2, 2014 at 7:03 PM, Mayne, Christopher G <cmayne2_at_illinois.edu<mailto:cmayne2_at_illinois.edu>> wrote:
Zeinab,

Please cc VMD-L so that others can learn from the discussion.

Hand editing PDB or PSF files is generally a bad idea. These formats are technically adhere to fixed-width specifications such that minor mistakes can easily result in broken files. My workflow in VMD typically looks like this:

1) load the PDB file into VMD

2) use VMD's atomselection mechanisms to modify atom name, type, charge, etc for each atom
e.g.,
set sel [atomselect top "index 0"]
$sel set name C1
$sel set type CG2R61
$sel set charge -0.115
$sel delete

3) check that VMD has correctly identified bonds. If it has made a mistake, use the "topo addbond <id1> <id2>" or "topo delbond <id1> <id2>" to fix the connectivity

4) once bonds are correctly defined, angles and dihedrals can automatically be determined via
topo guessangles
topo guessdihedrals

5) If you have any impropers, it is best to add those manually, although topotools can make a guess
topo addimproper <id1> <id2> <id3> <id4>

6) make sure you set the resname, chain, and segname as desired

7) tell VMD to update the topology
mol reanalyze top

8) write the psf/pdb
[atomselect top all] writepsf mymol.psf
[atomselect top all] writepdb mymol.pdb

typing "topo" with no arguments in VMD's tkcon will print an extensive usage message

Regards,
Christopher Mayne

On Oct 2, 2014, at 5:42 AM, Zeinab Emami wrote:

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 

--
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<tel:217-244-3349>
http://www.ks.uiuc.edu/Research/vmd/