(unknown charset) [AMBER] Bad atom type error during MMGBSA decomposition calsulations

From: (unknown charset) 王衍 <wangyanforward.gmail.com>
Date: Thu, 19 Dec 2013 16:47:06 +0800

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
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