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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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