Re: [AMBER] bad atom type: OA

From: Jason Swails <>
Date: Tue, 20 Jan 2015 12:21:29 -0500

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
               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
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Jan 20 2015 - 09:30:02 PST
Custom Search