Re: [AMBER-Developers] Proposed parm top addition

From: case <>
Date: Tue, 31 Jan 2012 21:12:43 -0500

On Tue, Jan 31, 2012, James Maier wrote:
> We have modified tleap to print ATOMIC_NUMBER and
> HYBRIDIZATION sections to the topology file.

I tend to agree with Jason here: hybridizations (at least for existing files)
are pretty unreliable, since they are really not used for very much, and hence
don't get checked and corrected.

The ATOMIC_NUMBER section is certainly useful for QM/MM and for other
things, like assigning GB radii. But programs that are going to use these
values should fall back on older methods (like looking at atom names or atom
types) in case that section is not present: we should continue to accept older
files and reproduce older behavior. That probably means (at least for this
release) of keeping the old GB radii code intact, and using it when
ATOMIC_NUMBER is not found in the prmtop; then having newer, simpler code if
that section *is* present. [Presumably, all prmtop files that have ff12SB
atom types will have been created by Amber12 can we enforce


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Received on Tue Jan 31 2012 - 18:30:03 PST
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