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 - 12:30:04 PST
