Mr. Simmerling,
Thank you for your suggestion.
The cross-term "region" (i.e., the atoms which needed cross-term parameters
between GAFF2 and FF14SB) participated in an amide bond with an amino acid,
so it made sense to me that parameters from the FF14SB force field
(parm10.dat) would be more appropriate than those from the GAFF2 force
field (gaff2.dat). As such, I directly matched the missing parameters to
their equivalents (or as close as could be found) in the parm10.dat file.
My conversions from missing cross-term parameters to parm10.dat parameters
are given below:
c-N -> C-N
o-c-N -> N-C-O
c-N-H -> C-N-H
c-N-CX -> C-N-CX
c3-c-N -> CT-C-N
o-c-N-H -> H-N-C-O
o-c-n-CX -> X-C-N-X
c3-c-N-H -> X-C-N-X
c3-c-N-CX -> X-C-N-X
The o-c-N-H dihedral in question (H-N-C-O from parm10.dat) has two
consecutive entries, as given below.:
H -N -C -O 1 2.50 180.0 -2. JCC,7,(1986),230
H -N -C -O 1 2.00 0.0 1.
J.C.cistrans-NMA DE
I initially only took the first line, but now knowing the meaning of the
negative periodicity, I took both lines into the .frcmod to define the
o-c-N-H dihedral. This stopped the error when saving the surfactant to
paramter topology and coordinate files.
As for your question, I took the parameters directly from the X-C-N-X entry
in parm10.dat, as given below:
X -C -N -X 4 10.00 180.0 2. AA,NMA
Should this "divider" term be modified beyond what is given in parm10.dat?
Much appreciated,
NDB
On Thu, Feb 24, 2022 at 9:00 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> the problem is that you've listed a negative periodicity for o-c-N-H, which
> tells it to read the next line into the same dihedral. However, your next
> line is the o-c-N-CX. So you need to either add more terms to o-c-N-H, or
> make the PN positive.
> as an aside, why do you use a divider of 4 for o-c-N-CX? It's unlikely that
> there are 4 sets of this term around that c-N bond.
>
> DIHE
> o-c-N-H 1 2.500 180.0 -2.000
> o-c-N-CX 4 10.000 180.0 2.000
>
>
> take a look at this for format details:
> https://ambermd.org/FileFormats.php#parm.dat
> --
> Carlos Simmerling, Ph.D. (he, him, his)
> Marsha Laufer Endowed Professor of Physical and Quantitative Biology
> Professor, Department of Chemistry
> Associate Director, Laufer Center for Physical and Quantitative Biology
> Room 119 Laufer Center, Stony Brook University, Stony Brook, NY 11794-5115
>
> http://www.simmerlinglab.org
>
> On Thu, Feb 24, 2022 at 9:50 AM Nathan Black <nathanblack262.gmail.com>
> wrote:
>
> > Hello AMBER Users,
> >
> > I recently posted here regarding the mixing of force fields (in my
> > specific case, GAFF2 and ff14SB) on a single residue. Thanks to the
> > assistance of of Dr. Anselm Horn and Mr. Carlos Simmerling, I was able to
> > develop a workflow that accomplishes this. However, I have run into a
> > separate issue during its implementation that I believe warrants its own
> > thread.
> >
> > I have written a .frcmod file that contains manually-input parameters at
> > the surfactant head-tail boundary. However, when trying to save parameter
> > topology and coordinate files for these surfactants in LEaP, I am given
> the
> > error:
> >
> > Error: **no torsion terms for o-c-N-CX.
> >
> > However, this parameter is accounted for in the .frcmod file I created. I
> > suspect I have formatted the file incorrectly, but then my other manual
> > torsion parameters are read without issue.
> >
> > I have attached a cleaned (single-attempt) leap.log file, as well as the
> > .frcmod file I wrote. Any assistance is much appreciated!
> >
> > -NDB
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Feb 24 2022 - 08:00:02 PST
