[gmx-users] Index file

Justin Lemkul jalemkul at vt.edu
Mon Dec 31 17:49:04 CET 2012

On 12/31/12 11:45 AM, Shima Arasteh wrote:
> It is 4.5.5.
> I need to say that I had a pdb file which was produced by VMD, May it be the reason of problem?

Without seeing the aforementioned information (substituting make_ndx screen 
output for editconf command, which is not relevant), it's impossible to say 
anything.  There is no logical reason why ions present in the coordinate file 
(independent of format) do not show up in the selection list and I cannot 
reproduce the problem with any file I have available.  Ions are showing up just 
fine in everything I can see.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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