VMD-L Mailing List

From: Wei Huang (whuang_at_cct.lsu.edu)
Date: Tue Feb 01 2011 - 16:22:28 CST

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!

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.
>