From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Feb 02 2011 - 09:26:32 CST

On Tue, Feb 1, 2011 at 11:04 PM, Wei Huang <whuang_at_cct.lsu.edu> wrote:
> 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".

this is a bug in topotools v1.0

you don't seem to have installed topotools v1.1
correctly because that bug it is fixed there.

> 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?

topotools v1.0 has too many bugs in the guess* functions
you want to make sure that you have topotools 1.1 installed
and working.

the alternative to installing it manually would be to install the
latest VMD 1.9 alpha test version.

please watch carefully the output of "package require topotools"
it has to say 1.1 not 1.0, or better yet use "package require topotools 1.1"

or even better and more paranoid yet, use a construct like this:

if {[catch {package require topotools 1.1} msg]} {
   vmdcon -error "$msg. This script requires at least TopoTools v1.1.
Exiting..."
   quit
}

cheers,
     axel.

>
> 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.
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.