VMD-L Mailing List

From: mohamad rahimi (rahimi992_at_yahoo.com)
Date: Sun Jan 30 2011 - 06:14:03 CST

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.

________________________________
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.