AMBER Archive (2009)

Subject: [AMBER] bad atom type: MN

From: Edward M (
Date: Mon Jun 22 2009 - 18:12:09 CDT


I am trying to change the amber9 file on sander mdread.f file
so I can include MN atoms. I was wondering if anyone could send me a paper
with the suggested parameters, perhaps this was taken care off on amber10?.
(i.e. can you provide the parameters).

I figured I just have to add a line after the MG, and define it.

Thanks a lot!.


            else if (atype == 'MG') 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
               ! The following values were taken from O.sp3 with
two bonded neighbors
               ! -> O has the smallest van der Waals radius
compared to all other
               ! elements which had been parametrized
               x(l170-1+i) = 0.49392d0
               x(l175-1+i) = -0.16038d0
               x(l180-1+i) = -0.00015512d0
               x(l185-1+i) = 0.00016453d0
               write( 0,* ) 'bad atom type: ',atype
               call mexit( 6,1 )
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