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.
Amber users that know more than I do should chime in here!
....dac
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Received on Mon Feb 18 2019 - 11:30:03 PST
