********>Bugfix 1:
Author: Dave Case
Date: 2/8/00

Programs: sander

Severity: generalized Born force field will refuse to run for proteins
          containing cysteine, perhaps for some other systems

Description: hydrogens bonded to Sulfur are treated as an error.

Note:  The patch below allows standard proteins with cysteine residues
       to be processed.  Some molecules that are not standard protein
       or nucleic acids may still fail and give this message.  We do
       not yet have any completely general workaround for this problem.

Fix:  apply the following patch to amber6/src/sander/mdread.f:

*** OLD mdread.f    Tue Feb  8 09:34:26 2000
--- NEW mdread.f    Tue Feb  8 09:33:59 2000
***************
*** 586,592 ****
                    atsymb2 = resat(i-j)(1:1)
                    if( atsymb2.ne.'H' ) go to 100
                  end do
!   100           if ( atsymb2.eq.'O' ) then
                    x(L97-1+i) = 0.8d0
                  else if (atsymb2.eq.'N') then
                    x(L97-1+i) = 1.2d0
--- 586,592 ----
                    atsymb2 = resat(i-j)(1:1)
                    if( atsymb2.ne.'H' ) go to 100
                  end do
!   100           if ( atsymb2.eq.'O' .or. atsymb2.eq.'S' ) then
                    x(L97-1+i) = 0.8d0
                  else if (atsymb2.eq.'N') then
                    x(L97-1+i) = 1.2d0


Temporary workarounds:  none

Files affected:  amber6/src/sander/mdread.f