VMD-L Mailing List
From: Mark Cunningham (cunningham_at_utpa.edu)
Date: Mon Feb 13 2012 - 09:15:18 CST
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- In reply to: lecan: "Meadionize"
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Luis:
VMD doesn't care about parameters but it does care
about topologies. You need to provide the topology
file not the parameter file.
Mark
-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of lecan
Sent: Sunday, February 12, 2012 9:05 PM
To: vmd-l_at_ks.uiuc.edu
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.
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- In reply to: lecan: "Meadionize"
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