Dear Amber Users/Devolopers,
I have performed MD simulations at constant pH (5.5). By visual
inspection of the resulting trajectory I have observed a favorable
interaction between an AS4 (as ASH for 55% of MD time) and another amino
acid in the biological counterpart.
To estimate the interaction between these residues I have used the
MM-GBSA/energy decomposition approach but, unfortunately, the total
energy of this interaction is positive (+0.5).
Is it possible that the MMPBSA.py script does not properly recognize ASP
as AS4? AS4 is bound to 4 hydrogens in the topology used for calculation...
Any suggestion will be appreciated.
Thanks.
Giovanni Grazioso
PhD, University of Milano (Italy)
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Received on Thu Apr 12 2018 - 07:30:02 PDT
