On Sat, Feb 1, 2014 at 11:27 AM, David A Case <case.biomaps.rutgers.edu>wrote:
>
> I wonder if we (i.e. James) can add another column in the MASS section for
> hybridization.
Done, in the same branch. (accepts sp3, sp2, sp1, and sp0~ corresponding to
the "0" hybridization)
A potential caveat:
LEaP might confuse the comment line with the hybridization, if the first
word matches a valid hybridization... so if you specify atomic number,
ensure the next string is the correct hybridization or gibberish
('aliphatic' would be fine, for instance).
As a bonus, many comments actually start with the hybridization of the atom
type, anyway.
Then we would not need to have the addAtomTypes section of the
> leaprc files
>
I made a leaprc.ff13SB sans addAtomTypes in the AtomicNumberAtomTypes
branch, as a proof of principle. It seems to work, though I've only tested
it on a few proteins familiar to me, so far.
> This may be a bit tricky: one has to be sure that any side effects of the
> "addAtomTypes" command are also done when the MASS section of the
> parm.dat file is read.
I haven't found any such side effects. Though given my limited
understanding of LEaP, that's not _necessarily_ a good sign...
I'll summarize my thoughts and code changes. If anything sounds suspect, I
invite whomever knows better to please chime in:
1. My understanding is that the sole purpose of addAtomTypes is to populate
vaAtomTypes (an array of atom type, element, and hybridization)
2. Information was previously taken from vaAtomTypes to complement the
information in Amber ParmSets via commands starting with iAtomType
3. grep tells me that the vaAtomTypes array and related iAtomType commands
are only used within amber.c ; my understanding is that their only purpose
is to populate GplAllParameters (which is referenced throughout LEaP).
4. I made the ...AmberReadParmSet... routines just bypass the iAtomType
commands that extract information from the vaAtomTypes array, whenever the
information is available from the MASS section.
James
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Received on Sat Feb 01 2014 - 21:00:02 PST
