From: Wei Huang (whuang_at_cct.lsu.edu)
Date: Tue Feb 01 2011 - 22:04:07 CST

On Feb 1, 2011, at 5:41 PM, Axel Kohlmeyer wrote:

> On Tue, Feb 1, 2011 at 5:22 PM, Wei Huang <whuang_at_cct.lsu.edu> wrote:
>> Hi all,
>>
>> I am following the instructions along this thread to convert my prmtop file to psf file.
>>
>> Here is the tcl script I use in the text mode:
>> mol new rna_wat.prmtop waitfor all
>> animate dup 0
>> set sel [atomselect top all]
>> $sel writepsf rna_wat.psf
>>
>> However, I got the following warning:
>> psfplugin) WARNING: PSF file is incomplete, no angles, dihedrals,
>> psfplugin) or impropers will be written.
>>
>> And in the psf file, I got nothing for angles, dihedrals and impropers
>> 0 !NTHETA: angles
>>
>>
>> 0 !NPHI: dihedrals
>>
>>
>> 0 !NIMPHI: impropers
>>
>> Could you help me figure out what the problem is? Thanks!
>
> the problem is that the reader for amber topologies does
> not support reading angle, dihedral and other definitions.
>
> now, if it is only about recreating the information that can be
> exported to the .psf file, you can use the scripts of the topotools
> plugin. however, a prmtop file - as the suffix already indicates -
> contains much more information, e.g. all force field parameters.
> those are currently not stored at all in VMD and would be lost
> when writing a .psf file regardless.
>
> if that doesn't matter, check out:
> http://sites.google.com/site/akohlmey/software/topotools
>
> i am presently in the process of expanding the documentation
> and writing some tutorials illustrating the usage; the descriptions
> on that webpage may already be sufficient to write a script that
> will generate a complete .psf file.
>
> cheers,
> axel.

Hi Axel,

Thanks for your reply.

I am trying to follow your instructions to write the script. Currently, I have some problems with topotools1.1. When I use the following commands:
topo guessdihedrals $sel
topo sortdihedrals $sel

I got the error message:
invalid command name "compareddihedrals".

But I can still get the list of dihedral angles.

This also happens to sortimpropers. But for sortangles, there is no problem.

BTW, is it okay to use the list of unsorted dihedral angles and improper angles in the psf file?

Best,
Wei
>
>>
>> Best,
>> Wei
>>
>>
>> On Jun 22, 2010, at 2:01 PM, Axel Kohlmeyer wrote:
>>
>>> On Tue, 2010-06-22 at 12:54 -0400, Lai zaizhi wrote:
>>>>
>>>> hi, John,
>>>> I use TkConsole, and the feedback information are following:
>>>>> mol new myfile.prmtop waitfor all
>>>> 0
>>>>> set sel [atomselect top all]
>>>> atomselect0
>>>>> $sel writepsf myfile.psf
>>>> atomsel:frame -1 out of range for molecule 0
>>>>
>>>> Any suggestions are very welcome. thanks
>>>
>>> just do an: animate dup 0
>>> right after the "mol new"
>>>
>>> axel.
>>>
>>>>
>>>>
>>>> On Tue, Jun 22, 2010 at 12:27 PM, John Stone <johns_at_ks.uiuc.edu>
>>>> wrote:
>>>> Hi,
>>>> I think what you actually want to do is this:
>>>>
>>>> mol new myfile.prmtop waitfor all
>>>>
>>>> set sel [atomselect top all]
>>>> $sel writepsf myfile.psf
>>>>
>>>> Let me know if you need further help with this.
>>>>
>>>> Cheers,
>>>> John Stone
>>>> vmd_at_ks.uiuc.edu
>>>>
>>>>
>>>>
>>>> On Tue, Jun 22, 2010 at 11:34:23AM -0400, Lai zaizhi wrote:
>>>>> hi, John, thanks for your reply. Another question is how
>>>> to save prmtop as
>>>>> psf file, I tried
>>>>>
>>>>> mol new myfile.prmtop waitfor all
>>>>> animate write psf myfile.psf waitfor all
>>>>>
>>>>> But it seems that it doesn't work:-(
>>>>>
>>>>> the system shows:
>>>>> info> save trajectory: 0 frame specified; no coordinates
>>>> written.
>>>>> On Mon, Jun 21, 2010 at 8:14 PM, John Stone
>>>> <johns_at_ks.uiuc.edu> wrote:
>>>>>
>>>>> If you just need partial charges, that ought to be
>>>> preserved
>>>>> when writing out as PSF in VMD. Let us know if you
>>>> need more help.
>>>>>
>>>>> Cheers,
>>>>> John
>>>>> On Mon, Jun 21, 2010 at 06:33:07PM -0400, Lai zaizhi
>>>> wrote:
>>>>>> hi, John, thanks! What I need from the PSF file is
>>>> the point charge
>>>>>> information.
>>>>>>
>>>>>> On Mon, Jun 21, 2010 at 5:56 PM, John Stone
>>>> <johns_at_ks.uiuc.edu>
>>>>> wrote:
>>>>>>
>>>>>> Hi,
>>>>>> You probably can't use VMD to do the kind of
>>>> conversion I expect
>>>>>> you are looking for (100% transfer of all info
>>>> from the prmtop
>>>>> file...)
>>>>>> While VMD will let you load the prmtop and save
>>>> it as a PSF, this
>>>>> would
>>>>>> likely not give you what you need to begin
>>>> simulating in NAMD.
>>>>> You'll
>>>>>> need to tell us more about what you intend to do
>>>> with the PSF
>>>>> file you
>>>>>> create.
>>>>>>
>>>>>> Cheers,
>>>>>> John Stone
>>>>>> vmd_at_ks.uiuc.edu
>>>>>> On Mon, Jun 21, 2010 at 05:41:37PM -0400, Lai
>>>> zaizhi wrote:
>>>>>>> On Mon, Jun 21, 2010 at 3:56 PM, Lai zaizhi
>>>>> <laizaizhi_at_gmail.com>
>>>>>> wrote:
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I have the amber topology file .prmtop
>>>> and .pdb file, now
>>>>> I want
>>>>>> to
>>>>>>> convert them to .psf file using vmd. What
>>>> should I do? I
>>>>> found
>>>>>> some
>>>>>>> archieves, yet they don't include more
>>>> details, and I also
>>>>> check
>>>>>> the
>>>>>>> manual of psfgen. It seems like psfgen
>>>> has no command to
>>>>> convert
>>>>>> prmtop
>>>>>>> to psf. Any suggestions will be very
>>>> welcome! thanks!
>>>>>>>
>>>>>>> Good day!
>>>>>>> zaizhi lai
>>>>>>
>>>>>> --
>>>>>> NIH Resource for Macromolecular Modeling and
>>>> Bioinformatics
>>>>>> Beckman Institute for Advanced Science and
>>>> Technology
>>>>>> University of Illinois, 405 N. Mathews Ave,
>>>> Urbana, IL 61801
>>>>>> Email: johns_at_ks.uiuc.edu Phone:
>>>> 217-244-3349
>>>>>> WWW: http://www.ks.uiuc.edu/~johns/ Fax:
>>>> 217-244-6078
>>>>>
>>>>> --
>>>>> NIH Resource for Macromolecular Modeling and
>>>> Bioinformatics
>>>>> Beckman Institute for Advanced Science and Technology
>>>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL
>>>> 61801
>>>>> Email: johns_at_ks.uiuc.edu Phone:
>>>> 217-244-3349
>>>>> WWW: http://www.ks.uiuc.edu/~johns/ Fax:
>>>> 217-244-6078
>>>>
>>>>
>>>> --
>>>>
>>>> NIH Resource for Macromolecular Modeling and Bioinformatics
>>>> Beckman Institute for Advanced Science and Technology
>>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>>>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>>>>
>>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
>>> http://sites.google.com/site/akohlmey/
>>>
>>> Institute for Computational Molecular Science
>>> Temple University, Philadelphia PA, USA.
>>>
>>
>>
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.