Dear amber users,
There is a bromine atom in my molecule and a error occur during MMGBSA
decomposition calculations. Here is the error message:
bad atom type: br
There are some other guys who come up with same error as I have. It seems
the only thing to do is just add the bromine atom message in the mdread.f
file and re-complied sander. But I have tried many many times, the error is
still there. Here is what I have added in the mdread.f file:
According to the mailing list, there are two places that needed to add
the radii information.
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
else
! write( 0,* ) 'bad atom type: ',atype
! call mexit( 6,1 )
x(l165-1+i) = 1.70 + 1.4;
x(l170-1+i) = 0.51245;
x(l175-1+i) = -0.15966;
x(l180-1+i) = -0.00019781;
x(l185-1+i) = 0.00016392;
write(6,'(a,a)') 'Using carbon SA parms for atom type', atype
has been changed to:
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
else if (atype(1:1) == 'BR' .or. atype(1:1) == 'br' .or.
atype(1:1) == 'BR1') then
! Br added by Amber-99 radii: Bondi radius and parameters
from P default
x(l165-1+i) = 1.978d0 + 1.4d0
x(l170-1+i) = 0.3865d0
x(l175-1+i) = -0.18249d0
x(l180-1+i) = -0.0036598d0
x(l185-1+i) = 0.0004264d0
else
! write( 0,* ) 'bad atom type: ',atype
! call mexit( 6,1 )
x(l165-1+i) = 1.70 + 1.4;
x(l170-1+i) = 0.51245;
x(l175-1+i) = -0.15966;
x(l180-1+i) = -0.00019781;
x(l185-1+i) = 0.00016392;
write(6,'(a,a)') 'Using carbon SA parms for atom type', atype
*the other place *
else if (atype == 'MG' .or. 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
else
write( 0,* ) 'bad atom type: ',atype
call mexit( 6,1 )
end if ! atype(1:1) == 'N'
x(L170-1+i) = 0.0d0
x(L175-1+i) = 0.0d0
x(L180-1+i) = 0.0d0
x(L185-1+i) = 0.0d0
has been changed to:
else if (atype == 'MG' .or. 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
else if (atype(1:1) == 'BR' .or. atype(1:1) == 'br' .or.
atype(1:1) == 'BR1') then
! Br added by Amber-99 radii: Bondi radius and parameters
from P default
x(L165-1+i) = 1.978d0 + 1.4d0
else
write( 0,* ) 'bad atom type: ',atype
call mexit( 6,1 )
end if ! atype(1:1) == 'N'
x(L170-1+i) = 0.0d0
x(L175-1+i) = 0.0d0
x(L180-1+i) = 0.0d0
x(L185-1+i) = 0.0d0
The is error still there whenever I run the decomposition calculation.
Could someone kind enough to tell me how to fix it?
Many thanks in advance!
--
===================================
*Yan WANG*
Ph.D. Candidate
State Key Lab of Theoretical & Computational Chemistry
Institute of Theoretical Chemistry
Jilin University
Changchun, 130023
P.R. China
Tel.+86-159-4308-8043
Email: wangyanforward.gmail.com
====================================
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Received on Thu Dec 19 2013 - 01:00:02 PST
