********>Bugfix 42:
Author: Ross Walker and Mike Crowley
Date: 03/29/2005
 
Programs: tleap, xleap
 
Description: The bond command used to use # for triple bonds but some
             machines treated # as a prefix to a comment in leap resulting
             in it being impossible to create a triple bond. This bugfix
             replaces the -, =, #, : options to the bond command with more
             obvious S,D,T,A options which specify single, double, triple
             and aromatic bonds respectively. This set of options should
             work on all architectures. Check the manual errata page for
             updates to the leap manual arising from this bugfix.
 
Fix:  Apply the following patch to 
         $AMBERHOME/src/leap/src/leap/commands.c
         $AMBERHOME/src/leap/src/leap/helptext.text
 
------------------------------------------------------------------------------
--- commands.c	2005-03-29 15:44:32.000000000 -0800
+++ commands.c	2005-03-29 15:44:17.000000000 -0800
@@ -1163,7 +1163,7 @@
 char            *sCmd = "bond";
 
    if ( iArgCount == 2 ) {
-        cOrder = '-';
+        cOrder = 'S';
         if ( !bCmdGoodArguments( sCmd, iArgCount, aaArgs, "a a" ) ) {
             VP0(( "usage:  bond   [order]\n" ));
             return(NULL);
@@ -1182,20 +1182,20 @@
     aB = (ATOM)oAssocObject(aaArgs[1]);
   
     switch ( cOrder ) {
-        case '-': 
+        case 'S': 
             iOrder = BONDSINGLE;
             break;
-        case '=': 
+        case 'D': 
             iOrder = BONDDOUBLE;
             break;
-        case '#': 
+        case 'T': 
             iOrder = BONDTRIPLE;
             break;
-        case ':': 
+        case 'A': 
             iOrder = BONDAROMATIC;
             break;
         default:
-            VP0(( "%s: Illegal bond order, no bond made.\n", sCmd ));
+            VP0(( "%s: Unknown bond order, no bond made.\n Valid bond orders are: S, D, T or A\n", sCmd ));
             goto DONE;
     }
     AtomBondToOrder( aA, aB, iOrder );

--- helptext.text	2005-03-29 15:44:32.000000000 -0800
+++ helptext.text	2005-03-29 15:44:24.000000000 -0800
@@ -264,7 +264,7 @@
 
 Create a bond between _atom1_ and _atom2_.  Both of these ATOMs must
 be contained by the same UNIT. By default, the bond will be a single
-bond.  By specifying "-", "=", "#", or ":" as the optional argument
+bond.  By specifying "S", "D", "T", or "A" as the optional argument
 _order_ the user can specify a single, double, triple, or aromatic
 bond.

------------------------------------------------------------------------------
 
Temporary workarounds: avoid needing to create triple bonds in leap.