On Tue, 2015-01-20 at 09:55 -0500, Brent Krueger wrote:
> I'll just make a small amendment to Jason's suggestion, which is that the
> atom type OA describes an oxygen, so probably one of the oxygen types would
> be more appropriate than carbon. OA is an aromatic heterocyclic oxygen, so
> I would guess that the ether OS would probably be the best radius to use.
I was under the impression that this was not one of the "main" elements
(C, N, O, H, or S). If OA is properly recognized as an oxygen, this
error should not occur. Here is the relevant code from sander's
mdread.F90 in Amber 12:
if (atomicnumber .eq. 7) then
x(L165-1+i) = 1.55d0 + 1.4d0
else if (atomicnumber .eq. 6) then
x(L165-1+i) = 1.70d0 + 1.4d0
else if (atomicnumber .eq. 1) then
x(L165-1+i) = 1.20d0 + 1.4d0
else if (atomicnumber .eq. 8) then
x(L165-1+i) = 1.50d0 + 1.4d0
else if (atomicnumber .eq. 15) then
x(L165-1+i) = 1.80d0 + 1.4d0
else if (atomicnumber .eq. 16) then
x(L165-1+i) = 1.80d0 + 1.4d0
else if (atomicnumber .eq. 12) then
! Mg radius = 0.99A: ref. 21 in J. Chem. Phys. 1997, 107, 5422
! Mg radius = 1.18A: ref. 30 in J. Chem. Phys. 1997, 107, 5422
! Mg radius = 1.45A: Aqvist 1992
x(L165-1+i) = 1.18d0 + 1.4d0
else
write( 0,* ) 'bad atom type: ',atype
call mexit( 6,1 )
end if ! atype(1:1) == 'N'
If this is indeed an oxygen atom and is recognized as such (i.e., its
atomic number is assigned to 8), then it should never hit the "bad atom
type" code path...
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jan 20 2015 - 09:30:02 PST
