On Thu, Aug 04, 2022, Kellon Belfon via AMBER wrote:
>
>The changes were made to have the atom names match up with the .cif format
>for the residues. For NME this was the change from CH3, HH31/2/3 to C,
>H1/2/3.
Put another way, Amber is now using the "official" (PDB) atom names for for
NME. Given that there are 30,000+ components (residues) in the PDB, any other
choice seems to invite chaos. And trying to make this "backward compatible"
seems to lead to more confusion that it is worth. (As an example, we still
allow the ancient "Na+" name instead of "NA" for the sodium ion. My view is
that this is actually a disservice to users, who would be better of being
forced to use the correct names.)
It would be possible to ignore the user's input residue and atom names, and
write code to just figure out what is going on based on the geometry and
element information. This is what the "prepareforleap" action in cpptraj does
for carbohydrates, where Amber internally uses non-standard names. Extending
this to other types of residues would probably require some deep-learning
approach. Volunteers are of course welcome....
.....dac
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Received on Thu Aug 04 2022 - 13:38:14 PDT
