Thanks Jason. That explains it perfectly!
> On Apr 8, 2022, at 9:35 AM, Jason Swails <jason.swails.gmail.com> wrote:
>
> Hi Max,
>
> The places you saw atom types being checked for `C1`, `C2`, and `C3` are
> from GB radii assignment algorithms taken from tleap. You'll also notice
> that alongside these type name checks are also checks about the atomic mass
> of that carbon being >=13, 14, and 15, respectively.
>
> Indeed tleap handled UA (united atom) force fields this way -- C1 types
> "swallowed" one hydrogen atom, C2 types swallowed 2, and C3 types swallowed
> 3. But such force fields have fallen out of favor, and I haven't heard of
> a new one in Amber being worked on in at least the past 15 years.
>
> I put in the extra checks in ParmEd for the mass because the assumption
> that the C1/C2/C3 atom types would only be used for UA force fields can
> only be guaranteed when operating completely within Amber (that is
> converting from another program's file types may very well use those atom
> type names -- and often do), so checking that the mass is at least equal to
> the sum of the mass of the carbon and assumed hydrogen atoms allows me to
> avoid false positives. And since UA force fields have no hydrogen atoms
> attached to those carbons, h-mass repartitioning (which would lower the
> masses and yield false negatives) doesn't apply to those atoms, anyway.
>
> HTH,
> Jason
>
> On Thu, Apr 7, 2022 at 4:30 PM Maximilian Ebert <max.ebert.me.com> wrote:
>
>> Hi everyone,
>>
>> In $AMBERHOME/AmberTools/src/parmed/parmed/tools/changeradii.py there is
>> an if statement checking for the atom type C1, C2 or C3. I couldn’t find
>> this atom types in the AMBER force fields. I found a definition in the
>> united-atom carbon types (
>> http://www.uoxray.uoregon.edu/local/manuals/biosym/discovery/General/Forcefields/AMBER.html
>> <
>> http://www.uoxray.uoregon.edu/local/manuals/biosym/discovery/General/Forcefields/AMBER.html>).
>> Could someone tell me what carbon atoms we look for at this place?
>>
>> Thanks,
>> Max
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>>
>
>
> --
> Jason M. Swails
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Received on Fri Apr 08 2022 - 17:30:02 PDT
