Dear fellow Amber developers,
Since we recently decided to allow atom types that end with the element
rather than start with the element (e.g., 2C, 3C), we realized that parts
of sander/pmemd that assign GB parameters based on atom type needed to be
reworked. Some of this code used just the first character of atom type.
Others compared to CT to figure out if the atom was an sp3 carbon, or if
not, some other kind of carbon or whatever other element. But as of ff10,
we have CX and CI as additional sp3 carbons, and more on the way. And
these atom types produced different results because of the way parameters
were assigned.
Since atom types must have element and hybridization information included
in the leaprc file and this information was already being loaded by tleap,
we thought that writing this information to the topology file for use by
sander, pmemd, or other programs was a natural way of accommodating new
atom types and determining element without having to rewrite lots of code
in the future. We have modified tleap to print ATOMIC_NUMBER and
HYBRIDIZATION sections to the topology file. Samples:
%FLAG ATOMIC_NUMBER
%FORMAT(10I8)
7 1 1 1 6 1 6 1 1
6
1 1 6 1 1 6 1 1 7
1
1 1 6 8 7 1 6 1 6
1
6 1 1 1 6 1 1 1 6
8
7 1 6 1 6 1 1 6 6
1
...
%FLAG HYBRIDIZATION
%FORMAT(10I8)
3 3 3 3 3 3 3 3 3
3
3 3 3 3 3 3 3 3 3
3
3 3 2 2 2 3 3 3 3
3
3 3 3 3 3 3 3 3 2
2
2 3 3 3 3 3 3 2 2
3
...
We modified sander and pmemd to read these sections and use the information
for parameter assignment. As one might expect, with the new code, the GB
results are the same whether using CT, CX, or 2C.
We wanted to present this to the developer's list for two reasons. First,
we'd like everyone else to know about this development and have a chance to
discuss before we think about pushing the changes. Second, while we're
proposing an addition to the parm top specification, we'd like to invite
everyone to think about other information that could be useful in our
topology files.
Thank you,
James Maier
Hai Nguyen
Carlos Simmerling
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Received on Tue Jan 31 2012 - 12:00:03 PST
