********>Bugfix 8:
Authors: Junmei Wang
Date: 05/05/2004

Programs: antechamber

Description: When the input is a mol2 file ("-fi mol2") antechamber, and
             the "-j 5" flag is also set, antechamber can give the
             wrong atom types or charges.

Fix:  Apply the following patch to $AMBERHOME/src/antechamber/bondtype.C

------------------------------------------------------------------------------
*** bondtype.C	2004/04/28 23:30:19	1.8
--- bondtype.C	2004/05/04 23:21:46
***************
*** 49,54 ****
--- 49,55 ----
  int *va_best;
  int *conjatom;
  int maxaps;
+ int judge_flag = 0;
  
  struct Point {
  	int addr;
***************
*** 731,739 ****
  {
  	int i, j, k;
  	int bondi, bondj;
! 	int flag, flag1, flag2;
  	int num;
  	int index[6];
  	for (i = 0; i < bondnum; i++) {
  		bondi = bond[i].bondi;
  		bondj = bond[i].bondj;
--- 732,762 ----
  {
  	int i, j, k;
  	int bondi, bondj;
! 	int flag, flag0, flag1, flag2 ;
  	int num;
  	int index[6];
+ 	if (judge_flag == 0) {
+ 		for (i = 0; i < bondnum; i++) {
+ 			if(bond[i].type != 10) 
+ 				continue;
+ 			bondi = bond[i].bondi;
+ 			bondj = bond[i].bondj;
+ 			flag0 = 0;
+ 			for (j = 0; j < bondnum; j++) {
+ 				if(i==j) continue;
+ 				if(bond[j].bondi == bondi || bond[j].bondj == bondi ||
+ 				   bond[j].bondi == bondj || bond[j].bondj == bondj) 
+ 					if(bond[j].type == 2 || bond[j].type == 8) {
+ 						flag0 = 1;
+ 						break;
+ 					}
+ 			}
+ 			if(flag0 == 0)
+ 				bond[i].type = 8;
+ 			else
+ 				bond[i].type = 7;
+ 		}
+ 	}
  	for (i = 0; i < bondnum; i++) {
  		bondi = bond[i].bondi;
  		bondj = bond[i].bondj;
***************
*** 883,889 ****
  	int tmpint1, tmpint2;
  	int tmp_addr, tmp_penalty, tmp_valence;
  	int flag = 0;
- 	int judge_flag = 0;
  
  	if (strcmp(COLORTEXT, "YES") == 0 || strcmp(COLORTEXT, "yes") == 0) {
  		if (argc == 2
--- 906,911 ----

------------------------------------------------------------------------------

Temporary workarounds: use pdb format files as input to antechamber, rather
                       than mol2 files