Re: [AMBER-Developers] Proposed parm top addition

From: Jason Swails <>
Date: Tue, 31 Jan 2012 22:18:54 -0500

On Jan 31, 2012, at 9:12 PM, case <> wrote:

> 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
> that?]

It'll be released with Amber 12. The only way that will be circumvented is if someone steals the ff12 file and uses it with an older leap rather than just building the (free and easy to install) AmberTools 12. I don't think this is likely to happen, especially when we stop supporting old AmberTools immediately after a new release. Is this good enough, though?

> ....dac
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Received on Tue Jan 31 2012 - 19:30:02 PST
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