VMD-L Mailing List

From: Ф¸»¹ó (helitrope_at_163.com)
Date: Wed May 01 2013 - 14:25:37 CDT

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