********> bugfix.11
Author: Junmei Wang
Date: 08/21/2009

Programs: antechamber

Description: fix the assignement of am1-bcc bond types in SO2 and NO2 groups

Usage: Use this patch to update amber10/src/antechamber/bondtype.c:

------------------------------------------------------------------------------
--- bondtype.c.orig	2008-05-22 00:22:01.000000000 -0400
+++ bondtype.c	2009-08-21 08:45:57.000000000 -0400
@@ -314,7 +314,9 @@
 		conjatom[i] = 0;
 		if (index1 >= 2 || index2 >= 2)
 			conjatom[i] = 1;
-		if (index3 >= 2 || index4 >= 3)
+        /* index3 >= 3 implies that S=O bonds in SO2 will not be delocalized;
+           index6 >= 2 makes NO2 bonds delocalized  */
+		if (index3 >= 3 || index6 >= 2)
 			conjatom[i] = 1;
 		for (;;) {
 			if (fgets(line, MAXCHAR, fp) == NULL)
------------------------------------------------------------------------------
Workarounds: none