> This already exists to some extent in LEaP. Each atom knows about its
> hybridization, number of bonded partners, and atomic number. Hopefully
> this is enough to unambiguously assign GB parameters?
>
Just want to point out, it seems atom types C1, C2, and C3 are the only
exceptional (2.2 Å) carbon radii. They seem to be in united atom libraries
({dna,protein}.amberua.lib, uni_amino03.lib) and then
residues.RNA.parmCHI_YIL.bsc.lib and, naturally, all_amino94ildn.lib. They
seem to be mistakenly different in ILDN, perhaps it's the same for the
nucleic acid chi modification?
If it's an artifact from united atom models (does anyone still use these?),
perhaps we can, as a band-aid, just delete the 'if(...)' and 'else ...'
around the 1.7 Å carbon assignment in leap?
(see lines 5883-5888 in unitio.c if curious)
Otherwise, perhaps there's some way to check for a united atom model--fewer
bonds than hybridization would suggest or something...
James
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Received on Fri Nov 01 2013 - 11:30:03 PDT
