Hello AMBER Users,
I am a new graduate student that is relatively unacquainted with AMBER.
As part of my research, I am attempting to simulate anionic surfactants
whose head(s) are standard amino acid residues, and whose tails are based
upon undecylenic acid (general organic domain). As such, I am hoping that
there is a way to model each surfactant such that the tail parameters are
defined by GAFF2, while the head parameters are defined by ff19SB.
It was my initial impression that the parmchk2 program could be used to
accomplish this, but the more I read through the Amber 20 manual, the less
confident I am that parmchk2 can "satisfy" missing parameters at the
surfactant head-tail boundary. It seems that parmchk2 is intended for use
in molecules with nonstandard residues but will still be described by a
single force field.
Is there any software or some other methodology that would allow me to
successfully implement this mixing of force fields without compromising the
integrity of any subsequent MD simulations? Any help/advice is much
appreciated!
-NDB
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Received on Sat Feb 19 2022 - 11:30:02 PST
