[AMBER] Include bound ions as part of the receptor molecule in MMPBSA.py

From: Nanjie Deng <nanjie.deng.gmail.com>
Date: Wed, 5 Dec 2018 16:27:11 -0500

We are trying to run MMPBSA.py in Amber18 on a DNA-ligand-ion complex
trajectory. There are two bound K+ ions inside the DNA which we want to
include as part of the receptor molecule in the MMPBSA analysis. However,
the MMPBSA.py script always automatically treating the two ions as part of
the solvent and excluding them in the calculation, even as we explicitly
define receptor_mask to include the ions. Are there other work around to
include the ions in the MMPBSA post-processing in Amber?

Thanks. 

-- 
Nanjie Deng, Ph.D.
Assistant Professor
Department of Chemistry and Physical Sciences
Pace University
1 Pace Plaza, Room W337
New York, NY 10038-1598
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Received on Wed Dec 05 2018 - 13:30:02 PST
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