From: Mark Cunningham (
Date: Mon Feb 13 2012 - 09:15:18 CST


VMD doesn't care about parameters but it does care
about topologies. You need to provide the topology
file not the parameter file.


-----Original Message-----
From: [] On Behalf Of lecan
Sent: Sunday, February 12, 2012 9:05 PM
Subject: vmd-l: Meadionize

 Hi everybody,

 I'm trying to ionize a protein-DNA system with the plugin Meadionize in
 VMD with the parameter par_all27_prot_na.prm. It runs well at first, but
 then it stops with this last lines:
 unknown residue type CLA
 unknown residue type CLA
 Info: generating structure...
 unknown residue type SOD
 ERROR: failed on end of segment
 MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

 This failure occurs when Meadionize tries to make the ION segment. Does
 anybody know what could be the problem? I checked out the
 par_all27_prot_na.prm and it has the SOD and CLA ions defined.

 best regards,

 Luis L.