VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 03 2013 - 15:45:09 CDT

Josh,
  Can you send a note to the maintainers of that tutorial and
ensure that this issue gets addressed?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, May 01, 2013 at 03:40:40PM -0500, Josh Vermaas wrote:
> The error you are getting is caused by being in the wrong directory when a
> topology load command is called (in this case from inside cg-ionize.tcl).
> Within cg-ionize.tcl, you load in a topology on line 581. There doesn't
> happen to be a martini-ions.top file in the current working directory
> (which I think should be 05-scripts, right?), and so psfgen cannot find
> the file. Swapping lines 579 and 580, or copying martini-ions.top to your
> current working directory should fix the immediate problem.
> -Josh Vermaas
>
> On 05/01/2013 02:25 PM, D-CUR,>>^1o wrote:
>
> Dear all,
> I followed the steps in the tutorial of "residue-based coarse graining
> using MARTINI force field in NAMD" and i tried to repeat the tutorial of
> "membrane protein".
> The website of the tutorial is :
> http://www.ks.uiuc.edu/Training/Tutorials/spectop-index.html#martini
>
> Everything went fine before i ionized the system, and the error is:
> Unable to open topology file martini-ions.top
>
> Molecule destroyed by fatal error! Use resetpsf to start over.
>
>
> I checked the martini-ions.top whose content is:
>
> 27 1
> MASS 1 Qa 72.0
> MASS 2 Qd 72.0
> !ions
> !Na+ ion
> RESI NA 1.00
> ATOM NA Qd 1.00
> !K+ ion
> RESI K 1.00
> ATOM K Qd 1.00
>
> !Cl- ion
> RESI CL -1.00
> ATOM CL Qa -1.00
> !Mg++ ion
> RESI MG 2.00
> ATOM MG Qd 2.00
>
> !Ca++ ion
> RESI CA 2.00
> ATOM CA Qd 2.00
>
> !ZN++ ion
> RESI ZN 2.00
> ATOM ZN Qd 2.00
>
> ! end of ions
>
>
> So it seems that there is no problem in the martini-ions.top, could
> anyone give me a suggestion?
>
> BW
> Fugui 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
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