Re: [AMBER-Developers] Extension of the parm*.dat file format

From: <>
Date: Mon, 21 Jan 2013 16:15:08 -0500 (EST)

OK, I didn't realize that END was not pertaining to NONB but to the end of
the parameter set. Could've figured as much. I'm going through other
aspects of the tleap code and finding things I will need to edit, but the
inherent similarity of these data structures to the antiquated but still
processed HBond declarations (two atom types, two doubles, and a
description) is making it easier to figure out what I need to write.


> On Mon, Jan 21, 2013, wrote:
>> <Type 1> <Type 2> <R* pair> <Eps pair>
>> ...
>> END
>> One might ask why put it in parm*.dat rather than a frcmod file, but I
>> can
>> certainly check for the extension in frcmods as well.
> This section should be able to be in both parm.dat and frcmod files...the
> code
> for reading these two formats is essentially identical (I can help with
> the
> implementation) and there are cases where these terms indeed represent
> small
> changes from an existing ff, and hence "belong" in a frcmod file.
> [Aside: I'm not sure what the "END" command does above; all other sections
> of
> parm.dat files are terminated with a blank line, and, indeed, the NONB
> section
> is as well. I think(?) "END" means "end of the entire parameter set",
> allowing comments to be placed after that.]
> We might want to consider an extra flag (I think in the POINTERS section,
> but
> maybe not....) that is set if LJEDIT terms have been used. This would
> make it
> simpler for programs that don't support such extensions (e.g. the current
> codes) to exit immediately upon finding such a flag.
> There *is* some overlap with ParmEd functionality, but I agree that it is
> better for the capability to be folded into LEaP.
> ...dac
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Received on Mon Jan 21 2013 - 13:30:03 PST
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