********>Master Bugfix File - AmberTools bugfixes for version 1.3

Programs: AmberTools

Description: This is the master bugfix file for AmberTools-1.3. It
             contains all of the bugfixes released against version 1.3
             in a single patch script.

Usage: Save this file in your $AMBERHOME directory and then 
       apply this patch file to your distribution as follows:

cd $AMBERHOME
patch -p0 -N <bugfix.all

If you have already patched some files the patch program should realise this
and skip them. If you have trouble then you may need to apply each of the
bug fixes separately.

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********> bugfix 1
Author: Dave Case
Date:   7 January 2010

Programs: sqm

Severity: medium

Description:  The sqm program may fail on scf convergence for some molecules;
this patch makes this a fatal error for the stand-alone version of the code

Fix:  Apply the following fix to amber11/src/sqm/qm2_scf.f:

---------------------------------------------------------------------------
--- src/sqm/qm2_scf.f	2 Sep 2009 14:48:07 -0000	10.8
+++ src/sqm/qm2_scf.f	7 Jan 2010 14:34:54 -0000
@@ -388,14 +388,23 @@
     !the current unconverged density. This will mean the forces
     !are not accurate but in an MD simulation they may be good
     !enough to allow the user to get out of a potentially bad geometry.
+#ifdef SQM
+    write(6,'(/,''QMMM: ERROR!'')')
+#else
     write(6,'(/,''QMMM: WARNING!'')')
+#endif
     write(6,'(''QMMM: Unable to achieve self consistency to the tolerances specified'')')
     write(6,'(''QMMM: No convergence in SCF after '',i6,'' steps.'')') qmmm_nml%itrmax
+#ifndef SQM
     write(6,'(''QMMM: Job will continue with unconverged SCF. Warning energies'')')
     write(6,'(''QMMM: and forces for this step will not be accurate.'')')
+#endif
     write(6,'(''QMMM: E = '',E12.4,'' DeltaE = '',E12.4,'' DeltaP = '',E12.4)') escf, energy_diff, density_diff
     write(6,'(''QMMM: Smallest DeltaE = '',E12.4,'' DeltaP = '',E12.4,'' Step = '',i6,/)') &
                       smallest_energy_diff(1), smallest_energy_diff(2), sm_energy_diff_step_number
+#ifdef SQM
+    call mexit(6,1)
+#endif
   end if
 
   if (qmmm_nml%verbosity > 0 .and. converged .and. qmmm_mpi%commqmmm_master) then
---------------------------------------------------------------------------
Workarounds:  wait (much) longer for a failed job to quit

********> bugfix 2
Author: Romain Wolf
Date:   26 January 2010

Programs: pbsa

Severity: minor

Description:  This patch allows pbsa to work with halogen-containing molecules
using the gaff force field.

Fix:  Apply the following fix to amber11/src/pbsa/sa_driver.f

---------------------------------------------------------------------------
--- src/pbsa/sa_driver.f	4 Jan 2010 23:48:17 -0000	10.9
+++ src/pbsa/sa_driver.f	20 Jan 2010 16:03:07 -0000	10.10
@@ -520,6 +520,9 @@
            isymbl(iatm)(1:1) == 'n' .or. &
            isymbl(iatm)(1:1) == 'o' .or. &
            isymbl(iatm)(1:1) == 'p' .or. &
+           isymbl(iatm)(1:1) == 'f' .or. &
+           isymbl(iatm)(1:1) == 'b' .or. &
+           isymbl(iatm)(1:1) == 'i' .or. &
            isymbl(iatm)(1:1) == 's' ) radi(iatm) = rin(iatm)
    end do
 
---------------------------------------------------------------------------
Workarounds:  none