Dear Amber mailing list,
I am trying to calculate the energy of my solute particle. I stripped the trajectory of all solvent and saved the topology file with the option nobox. When I try to run sander with imin=5, I get the error "The system has extended beyond the extent of the virtual box". I have selected ntb=0 in my mdin file for input.
Could you help me figure out what I am doing incorrectly?
Thank you very much for your help.
Best, Kristin
Kristin D. Krantzman
Professor, Department of Chemistry and Biochemistry
College of Charleston
Charleston, SC 29424
(843) 953-3378
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Received on Fri Sep 18 2015 - 15:00:03 PDT
