********> bugfix.46
Author:   Bill Ross
Date:     10/3/95

Programs: Leap

Severity: Moderate

Problem:  Loading PREP files (loadamberprep command): does not detect 
          extra charges in CHARGE section, which can cause core dump 
          or memory corruption.


Fix:  Make the following change to amber.c:
----------------------------------------------------------------------
*** OLD amber.c
--- NEW amber.c
***************
*** 1209,1214
                  iRead = sscanf( sLine, "%lf %lf %lf %lf %lf", 
                                  &da[0], &da[1], &da[2],
                                  &da[3], &da[4] );
                  for ( i=0; i<iRead; i++ ) {
                      AtomSetCharge( PVAI( vaCoor, TREENODEt, iCharge )->aAtom,
                                          da[i] );

--- 1209,1215 -----
                  iRead = sscanf( sLine, "%lf %lf %lf %lf %lf", 
                                  &da[0], &da[1], &da[2],
                                  &da[3], &da[4] );
+                 if ( iRead<=0 ) break;
                  for ( i=0; i<iRead; i++ ) {
  		    if ( iCharge >= iIndex ) {
  			VP0((" WARNING - skipping extra charge in: %s\n",
***************
*** 1210,1215
                                  &da[0], &da[1], &da[2],
                                  &da[3], &da[4] );
                  for ( i=0; i<iRead; i++ ) {
                      AtomSetCharge( PVAI( vaCoor, TREENODEt, iCharge )->aAtom,
                                          da[i] );
                      iCharge++;

--- 1211,1221 -----
                                  &da[3], &da[4] );
                  if ( iRead<=0 ) break;
                  for ( i=0; i<iRead; i++ ) {
+ 		    if ( iCharge >= iIndex ) {
+ 			VP0((" WARNING - skipping extra charge in: %s\n",
+ 						sResidueDescription(rRes) ));
+ 			continue;
+ 		    }
                      AtomSetCharge( PVAI( vaCoor, TREENODEt, iCharge )->aAtom,
                                          da[i] );
                      iCharge++;
***************
*** 1214,1220
                                          da[i] );
                      iCharge++;
                  }
-                 if ( iRead<=0 ) break;
              }
          } else if ( strcmp( saStr[1], "IMPROPER" )==0 ) {
  	    int	problem = 0;

--- 1220,1225 -----
                                          da[i] );
                      iCharge++;
                  }
              }
          } else if ( strcmp( saStr[1], "IMPROPER" )==0 ) {
  	    int	problem = 0;
***************
----------------------------------------------------------------------

Temporary workarounds: make sure correct # of charges is in prep.in;
                       ideally, use per-atom-line charge format instead
		       of CHARGE section.

--