ahmet yıldırım wrote:
Dear Justin,
I have Fatal Errror:The solvent group Water is not continuous. I look at
gmx-users mailing list search. I also have the same problem.
You
said:(http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html)
It is exactly what I said; you've proven it. You have solvent, ligand, then
solvent. To use genion (as the program prints out at the prompt) you must have
a *continuous* group of solvent in order to embed ions. If you re-arrange the
coordinate file and [molecules] section of the topology, you can achieve this.
How can I do the re-arrange you said? Can you explain a little bit?
I don't know what there is to explain. Water must be continuous in both the
coordinate file and the topology in order to use genion. You haven't said
what's in your system or what you've done to it up to this point.
-Justin
Thanks
--
Ahmet YILDIRIM
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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