Hello,
I was trying to parameterize a nonstandard residue for constant pH MD in
Amber 14 and noticed that
$AMBERHOME/AmberTools/src/etc/cpinutils/residues.py script has been
primarily changed from the corresponding cpin_data.py in Amber 12 or older
version.
Specifically, in the old cpin_data.py, I only needed to get the "relene"
term, which I obtain from TI computation. I guess this term corresponds to
the _ReferenceEnergy term in the residues.py script in Amber 14. However,
in the residues.py, there are a couple additional terms that I need to
define: solvent_energies and dielec2_energies.
Would anyone be able to explain 1) what those terms mean; 2) how I can
obtain the values for each term; and 3) how they affect the total reference
energy? Thank you!
Thanks,
Olivia
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Received on Wed Aug 27 2014 - 13:00:03 PDT
