From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Jan 30 2011 - 08:54:59 CST

On Sun, Jan 30, 2011 at 7:14 AM, mohamad rahimi <rahimi992_at_yahoo.com> wrote:
> I am surprised because I only want to transfer the structure from atomistic
> to coarse graining and I don't think the topology file is necessary. I used
> the RBCG method and in the manual also didn't mention for the transfer of
> the structure the topology file is mandatory. If it is necessary could
> please tell me how can I load topology file to vmd and the topology of
> atomistic require or coarse grainning.

well, the error message you quoted indicates that the builder
script could not find the file with the coarse grained coordinates,
and since you already mentioned the warning, it would be
normal to try providing a psf file to see, if the problem persists.

how to load files into vmd is explained in the user'ls guide.

if you still have problems, you have to provide more detailed information
of what exactly you did, where your input is coming from and - ideally -
the files that you are using, so that somebody can crosscheck it.

axel.

>
> ________________________________
> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> To: mohamad rahimi <rahimi992_at_yahoo.com>
> Cc: vmd-l_at_ks.uiuc.edu
> Sent: Sun, January 30, 2011 12:53:54 PM
> Subject: Re: vmd-l: CG Builder
>
> On Sun, Jan 30, 2011 at 4:31 AM, mohamad rahimi <rahimi992_at_yahoo.com> wrote:
>> Dear all
>>
>> I just start to work with CG Builder. I tried coarse graining water
>> molecule
>> and used relationship given in cg-tools (water.cgc). I always received
>> this
>> warning " No PSF file loaded" and after accept it I received this error.
>
> the code already told you, that it most likely won't work
> without topology information (as provided by a PSF file),
> so why are you surprised that it fails?
>
> axel.
>
>
>> Unable to load file 'cg_water.pdb' using file type 'pdb'.
>> Unable to load file 'cg_water.pdb' using file type 'pdb'.
>>     while executing
>> "mol new "$::cggui::toCGoutpdbfile""
>>     (procedure "::cggui::buildResidueCGExecute" line 45)
>>     invoked from within
>> "::cggui::buildResidueCGExecute"
>>     invoked from within
>> ".cggui.toCGResidueFrame.applyDB invoke"
>>     ("uplevel" body line 1)
>>     invoked from within
>> "uplevel #0 [list $w invoke]"
>>     (procedure "tk::ButtonUp" line 22)
>>     invoked from within
>> "tk::ButtonUp .cggui.toCGResidueFrame.applyDB"
>>     (command bound to event)
>>
>> can anybody help me?
>>
>> Thanks
>> Mohammad
>>
>>
>>
>
>
>
> --
> 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.