Re: [AMBER-Developers] Proposed parm top addition

From: James Maier <>
Date: Wed, 1 Feb 2012 12:52:55 -0500

> > [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?

I think it's reasonable to expect that one would use the latest AmberTools
with ff12SB, but I donít know if that should be counted on. Unfortunately,
leap glosses over undefined commands so putting a version "require" command
in the leaprc file won't help to enforce, unless such a command actually
already exists and somehow escaped my attention.

Short of that, I think printing a warning if assigning GB (or other)
parameters without atomic numbers, as Jason suggested, is probably the best
option. Something like: "WARNING: Assigning GB parameters based on atom
types. This will lead to incorrect results if using later than ff10.
 Rebuild topology file with AmberTools 12 to remove this warning." At
least sander/pmemd will tell users what's happening.

The list of atom types in the GB parameter assignment code should then stop
at CI (bsc0) and CX (ff10).

To answer Jason's previous question about what the hybridization numbers
mean and possibly shed some light as to why H are sp3:

The values that I had leap print for hybridization were the integers that
leap used to store this information. This turned out to be 1 for sp1, 2
for sp2, and 3 for sp3---the number of p orbitals, as was suggested.
 Taking a second look, leap does not appear to recognize any other
hybridizations. If the hybridization information cannot be trusted, and
wonít be made accurate any time soon, it probably shouldn't be used to
assign parameters.

I was looking to hybridization because GBSA parameters were assigned based
on comparisons, for example, to CT---which I saw as the de facto sp3
carbon. I was thinking of the possibility of carbanions and other such
things, but perhaps they wouldn't be CT, anyway.

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Received on Wed Feb 01 2012 - 10:00:03 PST
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