Reasonable,
Thank you very much
On Mon, Feb 18, 2019 at 3:27 PM Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Feb 18, 2019 at 2:21 PM David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Mon, Feb 18, 2019, Hadi Rahmaninejad wrote:
> > >
> > >I am trying to create forcefield files from topology and coordinate
> file I
> > >got using "Parmed" and "chamber" command. The method I am using is by
> > >"writeFrcmod" command, which was recommended from another amber user
> here
> > >in mailing list. However, I am getting this error message: "ChamberParm
> > >objects are not supported by this action". I suspect if the reason is
> > >inorganic atom (Si) that I am using, but I am not sure. I appreciate if
> > >anyone can help me with this.
> >
> > OK...my apologies: I failed to realize the limitations of the
> > writeFrcmod action. My guess(!) is that the problem is not Si per se,
> > but is rather related to the fact that CHARMM force fields are supported
> > in a somewhat convoluted way in Amber, that cannot be back-ported to a
> > frcmod file.
> >
> > Stated another way: the chamber conversion is done via a low-level
> > (prmtop) manipulation, and there is no (current) way to translate this
> > back to a high-level (frcmod) file format. I suspect you may have to
> > re-build the system (say with a new solvent) in CHARMM, then re-run
> > parmed/chamber to get the updated Amber prmtop file.
> >
>
> I'll expand on this briefly:
>
> The CHARMM force field currently supports potential energy terms that
> aren't present in the typical AMBER force fields. The following come to
> mind:
>
> * Quadratic improper torsions
> * Urey-Bradley angle terms [1]
> * correction-map (CMAP) coupled torsion terms [1]
> * Modified 1-4 Lennard-Jones parameters
>
> [1] These terms *can* be represented in an frcmod file I think, but they
> are somewhat recent additions specifically for some of the polarizable
> force fields from ~5-10 years ago. I'm not aware of any efforts made to
> check that they implement an equivalent representation as CHARMM.
>
> Simply put, tleap is fundamentally incapable of reliably generating a
> system governed by the CHARMM family of force fields, and there exists no
> way of correctly expressing the parameters from a CHARMM system in an
> frcmod file. So instead of doing as much as it can (and risking that
> people inadvertently mistake the resulting files as the 'real' CHARMM force
> field), ParmEd simply refuses to try.
>
> HTH,
> Jason
>
>
> > Amber users that know more than I do should chime in here!
> >
> > ....dac
> >
> >
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> >
>
>
> --
> Jason M. Swails
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Received on Mon Feb 18 2019 - 13:30:01 PST
