[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
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Received on Mon May 15 2017 - 19:30:02 PDT
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