[gmx-users] make_ndx error

Justin Lemkul jalemkul at vt.edu
Sat Jan 26 19:51:27 CET 2013

On 1/26/13 1:49 PM, Albert wrote:
> On 01/26/2013 07:41 PM, Justin Lemkul wrote:
>> What types of ions do you have?  I can reproduce this problem for a protein
>> with ions bound to it, which are numbered discontinuously with water and ions
>> in solution.
>> -Justin
> thank you for kind reply.
> I only have Na+ and Cl-.

Can you please post the following:

1. The groups printed in the make_ndx prompt
2. The output of gmxcheck on an index file created from your coordinate file 
(created simply by typing 'q' at the prompt, i.e. not creating any special groups)



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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