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

From: David A Case <>
Date: Mon, 21 Jan 2013 15:55:06 -0500

On Mon, Jan 21, 2013, wrote:
> <Type 1> <Type 2> <R* pair> <Eps pair>
> ...
> 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 GPU
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.


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Received on Mon Jan 21 2013 - 13:00:03 PST
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