Dr. Horn and Other AMBER Users,
I would like to provide more context with regard to my methodology and
overarching research purpose. After describing my methodology in detail, I
will address the errors I have run into. My immediate goal is to simulate
interactions between polymerized micelles and organic ligands. At the
moment, my methodology begins with processing a .cif file corresponding to
the modified undecylenic acid-based tail, then adding the amino acid
residues in LEaP following the sequence {} command.
The process of the input .cif file begins with the use of *antechamber* to
perform charge assignments using the AM1-BCC method (-c bcc) and define
atom types by GAFF2 (-at gaff2), giving a .ac file output. From looking at
past files on my research computer, the (-at amber) command was given,
which as I understand corresponds to PARM data types rather than GAFF2.
Then, I used *prepgen* to omit hydrogen atoms as needed for polymerization
and addition of amino acid residues; the tail atom was defined (the head is
null) to facilitate the addition of amino acid headgroups. This gave a
.prepin file output.
After this, *parmchk2 *was used to generate force field modifications for
the surfactant tail, using the gaff2.dat force field parameter file as an
input (-p $AMBERHOME/dat/leap/parm/gaff2.dat). I will designate this
tail-based .frcmod file as *tail.frcmod.*
These force field modifications were loaded into LEaP, and the surfactants
are generated using the sequence {TAL AMR ... CAMR} command, where "TAL"
corresponds to the processed tail, and "AMR" corresponds to amino acid
residues; this command is performed after loading the leaprc.protein.ff19SB
force field.
Then, *parmchk2 *is run again on each combined surfactant residue, this
time using the parm19.dat force field parameter file as an input. I will
designate the output files as *surfactant.frcmod *files.
This concludes my process of surfactant generation in AMBER, other than
saving the result of the sequence {} command. As for the issues I have run
into, I have found that the *surfactant.frcmod *files have several "ATTN,
need revision" lines when following the above procedure. I have found that
when the same atom type and force field modification input (either GAFF2 or
PARM) is used for all *antechamber *and *parmchk2 *commands, there are
minimal "ATTN, need revision" lines.
In my potentially naive view, shouldn't I use *gaff2 *for the *antechamber* and
first *parmchk2 *step (as these steps correspond to the tail in the absence
of amino acid residues), followed by *parm19 *for the final *parmchk2 *
step?
Also, how would I go about manually determining inputs for any parameters
that *parmchk2 *is not able to determine? Are there recommendations given
for this in the AMBER manual?
Greatly appreciative,
NDB
On Mon, Feb 21, 2022 at 10:31 AM Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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Received on Mon Feb 21 2022 - 10:00:02 PST
