VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed May 01 2013 - 15:40:40 CDT

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, Ф¸»¹ó 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
>
> MASS1Qa72.0
> MASS 2Qd72.0
>
> !ions
> !Na+ ion
> RESI NA1.00
> ATOM NAQd1.00
>
> !K+ ion
> RESI K1.00
> ATOM KQd1.00
>
> !Cl- ion
> RESI CL-1.00
> ATOM CLQa-1.00
>
> !Mg++ ion
> RESI MG2.00
> ATOM MGQd2.00
>
> !Ca++ ion
> RESI CA2.00
> ATOM CAQd2.00
>
> !ZN++ ion
> RESI ZN2.00
> ATOM ZNQd2.00
>
> ! end of ions
>
> So it seems that there is no problem in the martini-ions.top, could
> anyone give me a suggestion?
> BW
> Fugui
>
>