Nathan,
parameterization is IMHO not the ideal task for getting started with MD,
especially if you intend to use the new ff19SB force field.
In principle, one can mix parameters of different force fields;
recommendations about that are given in the manuals: e.g. gaff(2) is
generally considered to be well suited to work with ff14SB.
However, if you use different force fields within the same residue
(protein + organic), you end up with different sets of atom types, i.e.
uppercase (protein) and lowercase (gaff), which requires special, mostly
manually defined cross-terms with mixed atom types (e.g. torsions); the
respective parameters may, however, be obtained from already existing
parameter lists.
Alternatively, one could use/add specialized protein atom types and just
import the then missing parameters from the other force field.
In your case, you had to decide whether your total system is more like a
protein with some non-standard amino acid residues, or like an organic
compound which has some similarity to a protein. Then you could choose
your 'main' force field accordingly.
In any case, you'd need to somehow validate your parameter assignment
via MD simulations to see whether they work as expected.
In my (limited) experience, many parameterizations or parameter
assignments involve manual steps and decisions that are not easily
performed automagically. It depends on your system and your research
question.
But others may chime in here and provide more helpful comments...
All the best
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
On 02/19/2022 08:04 PM, Nathan Black wrote:
> 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 Mon Feb 21 2022 - 09:00:02 PST
