Hello Jones,
As Ray mentioned above, the full parameter set of the pGM force field is
still under development. However, the tool sets for parameterizing
molecules with the pGM model are available in AmberTools23 now. You can
refer to this tutorial (
http://htmlpreview.github.io/?https://github.com/ShijiZ/PyRESP/blob/master/tutorial/pyresp.html)
to better understand how pGM parameterization works and play with your
interested molecules. You can also read the paper (
https://pubs.acs.org/doi/full/10.1021/acs.jctc.2c00230) about the pGM
parameterization program called PyRESP.
Thanks for your interest in the pGM model. Feel free to ask if you have any
questions.
Best regards,
Shiji Zhao
On Fri, Jul 21, 2023 at 8:28 AM Ray Luo via AMBER <amber.ambermd.org> wrote:
> Hi Jones,
>
> Thanks a lot for your interest! The very first pGM force field for
> proteins is still under development, though the code supporting pGM
> is ready.
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor of Structural Biology/Biochemistry/Biophysics,
> Chemical and Materials Physics, Chemical and Biomolecular Engineering,
> Biomedical Engineering, and Materials Science and Engineering
> Department of Molecular Biology and Biochemistry
> University of California, Irvine, CA 92697-3900
>
> On Fri, Jul 21, 2023 at 6:15 AM Jones De Andrade via AMBER
> <amber.ambermd.org> wrote:
> >
> > Hi all.
> >
> > Direct question: I just downloaded the last (22?) ambertools to study
> > its "newest and coolest" stuff. :)
> >
> > Among them, I'm the most interested in the pGM force field (which seems
> > to be supported).
> >
> > However, I want to read the force field files (by hand, as I usually do)
> > to see how it differs and get a better understand on it, but I'm not
> > finding them (at least, not in the usual dat/leap directory): what can I
> > be doing so wrongly? :(
> >
> > Thanks a lot in advance for any help!
> >
> > Jones
> > ---
> > Jones de Andrade
> > (jdandrade.iq.ufrgs.br)
> > DFQ/IQ/UFRGS
> > Lattes:
> https://urldefense.com/v3/__http://lattes.cnpq.br/6675936210583999__;!!CzAuKJ42GuquVTTmVmPViYEvSg!Miriz_3kurKLNf4Qn2UvXZGUHt03H8QRA35hk57TdBvWUrsYY26_g7IFSgJVzZEJYoHFSEtc-AZi5g$
> > Orcid:
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Received on Mon Jul 24 2023 - 09:30:02 PDT
