VMD-L Mailing List

From: Zeinab Emami (zemami_at_ku.edu.tr)
Date: Thu Oct 02 2014 - 11:48:49 CDT

Dear Christopher Mayne,

I really appreciate it. Your answer is so comprehensive and informative.
Thank you very much and good luck..

Sincerely Yours,
Zeinab

On Thu, Oct 2, 2014 at 7:45 PM, Zeinab Emami <zemami_at_ku.edu.tr> 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
> > 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/
>>
>>
>>
>
>