[AMBER] Reference structure for targeted MD

From: Francesco Gentile <fgentile.ualberta.ca>
Date: Mon, 15 May 2017 20:26:39 -0600

Hello everyone,
I am trying to run a targeted MD simulation. Reading the manual, it says
that both the reference and the input coordinates should match the prmtop
file. I am wondering how this can be done, as I don't expect to see the
same number of water molecules by solvating the two structures, even using
the same parameters for leap. Thanks in advance for your help, 
-- 
Francesco Gentile
PhD Candidate, Biophysics
CCIS 3-215, Department of Physics
7-112, Li Ka Shing Centre for Health Research Innovation
University of Alberta, Edmonton, AB T6G 2E1
Canada
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Received on Mon May 15 2017 - 19:30:02 PDT
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