Thank you for your help
I modified the code as suggested and it works fine now.
I also tried to install AmberTools14 with Amber12 as suggested in
http://jswails.wikidot.com/installing-ambertools-14-and-older-amber
. However, it seems that MMPBSA.py failed to access the sander module in
Amber12.
Best regards
On Tue, Jan 20, 2015 at 6:21 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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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>
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Received on Wed Feb 04 2015 - 04:30:03 PST
