********>Bugfix 13:
Author: Junmei Wang, reported by Kazua Ohta 
Date: 08/18/06

Programs: Antechamber

Description: The memory allocations for ind_valence and ind_bondnum with malloc
             have problems. The size should be atomnum not bondnum. This bug
             may cause problems for molecules that have a greater number of
             atoms than number of bonds.

Fix:  apply the following patch to amber9/src/antechamber/bondtype.C

------------------------------------------------------------------------------
*** bondtype.C	3 Apr 2006 23:34:26 -0000	9.0
--- bondtype.C	18 Aug 2006 21:38:57 -0000
***************
*** 1278,1289 ****
  		fprintf(stderr, "memory allocation error for *con_num\n");
  		exit(0);
  	}
! 	ind_bondnum = (int *) malloc(sizeof(int) * bondnum);
  	if (ind_bondnum == NULL) {
  		fprintf(stderr, "memory allocation error for *ind_bondnum\n");
  		exit(0);
  	}
! 	ind_valence = (int *) malloc(sizeof(int) * bondnum);
  	if (ind_valence == NULL) {
  		fprintf(stderr, "memory allocation error for *ind_valence\n");
  		exit(0);
--- 1278,1289 ----
  		fprintf(stderr, "memory allocation error for *con_num\n");
  		exit(0);
  	}
! 	ind_bondnum = (int *) malloc(sizeof(int) * atomnum);
  	if (ind_bondnum == NULL) {
  		fprintf(stderr, "memory allocation error for *ind_bondnum\n");
  		exit(0);
  	}
! 	ind_valence = (int *) malloc(sizeof(int) * atomnum);
  	if (ind_valence == NULL) {
  		fprintf(stderr, "memory allocation error for *ind_valence\n");
  		exit(0);
------------------------------------------------------------------------------

Temporary workarounds: none