Dear Amber Community,
I edited amber20_src/AmberTools/src/sander/mdread2.F90 to contain the following blocks for Fe, as recommended in a previous post. I still get the “Bad Atom Type” message after recompiling. What can I do to fix this issue?
if ( gbsa == 1 ) then
……
x(l185-1+i) = 0.00016453d0
else if (atype(1:1) == 'FE' .or. atype(1:1) == 'Fe' .or. atype(1:1) == 'Fe') then
! ref. Ebook: Molecular and Cellular Iron Transport By Douglas M. Templeton
! FE radius = 0.78A: FE2+ octahedral high spin
! FE radius = 0.610A: FE2+ octahedral low spin
! FE radius = 0.630A: FE2+ tetrahedral high spin
! FE radius = 0.640A: FE2+ square planner high spin
x(l165-1+i) = 0.78d0 + 1.4d0
……..
else if ( gbsa == 2 ) then
……..
x(L165-1+i) = 1.18d0 + 1.4d0
else if (atype(1:1) == 'FE' .or. atype(1:1) == 'Fe' .or. atype(1:1) == 'fe') then
x(l165-1+i) = 0.78d0 + 1.4d0
I’ve attached the edited mdread2.f90 to this message for reference.
Best,
Matthew
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Received on Sat Jul 03 2021 - 00:00:02 PDT
