Dr. Horn, Mr. Simmerling and other AMBER Users,
My intention for the second call of parmchk2 was to generate parameters for
atoms at the surfactant head-tail boundary. I might be able to more
concisely explain my current process here:
- Process surfactant tail .cif file into a format compatible with LEaP
(as described previously in the antechamber & prepgen steps) and generate
frcmod information with parmchk2.
- Load surfactant tail with frcmod information into LEaP, add amino acid
residues to form a headgroup with sequence {UNA ALA CLEU} as an example,
where "UNA" describes the loaded surfactant tail.
- Call parmchk2 again to generate frcmod information for the overall
surfactant. This step is intended to help define parameters at the
surfactant tail-head boundary, as this boundary did not exist at the time
that the first parmchk2 program was called (the amino acid headgroup was
not added yet).
This workflow is one I inherited from my predecessors, and while I have
read the entry for parmchk2 in Chapter 16 of the manual, I admittedly do
not have much of a dynamic understanding of these programs. The exact
workflow I inherited uses (-at amber) in the antechamber step and (-p
$AMBERHOME/dat/leap/parm/parm19.dat) for all subsequent parmchk2 calls,
which in my understanding should use PARM atom types exclusively throughout
the process and never GAFF2 (based on "Antechamber options" in page 301 and
"parmchk2" in page 304 of the Amber 2021 Manual). Is this assumption
correct?
In any case, I have modified the inherited workflow so that the antechamber
and first parmchk2 procedure calls gaff2 (-at gaff2) and (-p
$AMBERHOME/dat/leap/parm/gaff2.dat), respectively. The final parmchk2
procedure calls parm19.dat and is unchanged. Does this not accomplish the
desired effect of mixed force fields? If not, are there other changes that
you might recommend? I will peruse the modified amino acid residue tutorial
today as recommended. I have also reread the note given in the manual, and
will change my protein force field to FF14SB.
I will attempt the general workflow proposed by Dr. Horn, but before I do
so, I would like to ascertain that my workflow does, in fact, perform the
intended task of mixing GAFF2/FF19SB force fields.
A final question- how does one "generate" or otherwise determine new
parameters to implement in a new frcmod file (as suggested in step 2 of Dr.
Horn's proposed workflow) so that the system is fully defined?
Thank you so much for your assistance. It is much appreciated.
-NDB
On Mon, Feb 21, 2022 at 12:04 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> I'm not sure I understand your workflow and the goal of each step. If I
> understand correctly, you're generating parameters, then running leap to
> build the polymer, then generating parameters again? why do you need to
> generate the 2nd frcmod? if it's to make the cross terms, this doesn't seem
> like the best way since it will also try to generate parameters for the
> amino acids, and probably redo the once in your initial frcmod. maybe it's
> just not clear what you're using as input the second time - are you just
> using parm19.dat and not GAFF or anything else?
>
> As Anselm suggested, you likely want to generate parameters for the new
> residue using GAFF or something like that, and make the cross terms between
> GAFF and the protein model, and then use that frcmod in leap to build the
> system. I don't see a need for redoing the frcmod after you've already done
> it once.
> Others may be more familiar with this type of workflow and have better
> suggestions. The modified amino acid tutorial on the main Amber web site
> may also be helpful.
>
>
> On Mon, Feb 21, 2022 at 12:55 PM Nathan Black <nathanblack262.gmail.com>
> wrote:
>
> > 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
> > > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 22 2022 - 09:30:02 PST
