********>Bugfix 29:
Prepared by: Ray Luo & Meng-Juei Hsieh
Date: 11/27/2009

Programs: mm_pbsa

Description:
    We have found a workaround of a bug in mm_pbsa of amber10. This
    bug was reported by Gianluca Degliesposti to amber mailinglist:
    PB's ECAVITY term would have been scaled twice if MS was set to
    0. Following the hint in the GB part of the mm_pbsa script, the
    surface tension should be set to 1.0. 

    This patch has been tested in the original amber10. (Note: test
    case failure: 04_MMPBSA_Nmode/ras_raf_II_wt_statistics.out.dif 
    is expected.) 

Usage: Save this file in your $AMBERHOME directory and then apply this patch 
       file to your amber10 distribution as follows:

cd $AMBERHOME
patch -p0 -N -r patch_rejects < bugfix.29

Index: src/mm_pbsa/mm_pbsa_createinput.pm
===================================================================
--- src/mm_pbsa/mm_pbsa_createinput.pm	(original)
+++ src/mm_pbsa/mm_pbsa_createinput.pm	(new copy)
@@ -580,7 +580,10 @@
     print OUT "  istrng = ${istrng},       radiopt = ${radiopt},\n";
     print OUT "  sprob  = ${sprob},     space   = ${space},\n";
     print OUT "  maxitn = ${maxitn},    npopt   = ${npopt},    dbfopt  = 1,\n";
-    print OUT "  cavity_surften = ${cavity_surften},    cavity_offset   = ${cavity_offset},\n";
+    # Surften is set to 1.0, so SAS is calc itself
+    #   -> calc of E(SAS) is done in statistics module
+    #print OUT "  cavity_surften = ${cavity_surften},    cavity_offset   = ${cavity_offset},\n";
+    print OUT "  cavity_surften = 1.0,    cavity_offset   = 0.0,\n";
     print OUT "  npbverb= 1\n";
     print OUT " &end\n";