********> bugfix.6
Author:   Bill Ross
Date:     4/21/02

Programs: Leap

Severity: Moderate

Description: Missing charges in a prep.in file result in non-0 charges
	     being assigned.

Fix: Make the following changes to amber.c:
-----------------------------------------------------------------------------
*** OLD amber.c	
--- NEW amber.c
***************
*** 854,860 ****
  ATOM            aMain0, aMain1;
  BOOL            bFirstTime;
  double          da[10];
! int             i, iLen, iErr, iCharge, iCharges = 0;
  double          dCutoff;
  INPUTLINEt	ilLine;
  int             iaTreeStack[500];
--- 854,860 ----
  ATOM            aMain0, aMain1;
  BOOL            bFirstTime;
  double          da[10];
! int             i, iLen, iErr, iCharge, iCharges = 0, iChgWarn = 0, iAtoms = 0;
  double          dCutoff;
  INPUTLINEt	ilLine;
  int             iaTreeStack[500];
***************
*** 1014,1019 ****
--- 1014,1020 ----
  	    continue;
  	}
          MESSAGE(( "Read atom: %s\n", saStr[2] ));
+ 	iAtoms++;
  
                  /* Create an entry in the vaCoor array */
  
***************
*** 1107,1116 ****
                  /* Get the coordinates for the atom */
  
          iBond = cPCoor->iBack;
!         if ( iRead == 8 ) {
  	    bStringToDouble( saStr[5], &dX );
  	    bStringToDouble( saStr[6], &dY );
  	    bStringToDouble( saStr[7], &dZ );
  	    bStringToDouble( saStr[8], &dCharge );
  	    iCharges++;
          } else {
--- 1108,1122 ----
                  /* Get the coordinates for the atom */
  
          iBond = cPCoor->iBack;
!         if ( iRead == 7 ) {
  	    bStringToDouble( saStr[5], &dX );
  	    bStringToDouble( saStr[6], &dY );
  	    bStringToDouble( saStr[7], &dZ );
+ 	    dCharge = 0.0;
+         } else if ( iRead == 8 ) {
+ 	    bStringToDouble( saStr[5], &dX );
+ 	    bStringToDouble( saStr[6], &dY );
+ 	    bStringToDouble( saStr[7], &dZ );
  	    bStringToDouble( saStr[8], &dCharge );
  	    iCharges++;
          } else {
***************
*** 1144,1150 ****
              dX = dVX(&vPos);
              dY = dVY(&vPos);
              dZ = dVZ(&vPos);
! 	    bStringToDouble( saStr[11], &dCharge );
          }
          if ( iIndex >= iVarArrayElementCount(vaCoor) ) {
              VarArraySetSize( vaCoor, iIndex+1 );
--- 1150,1163 ----
              dX = dVX(&vPos);
              dY = dVY(&vPos);
              dZ = dVZ(&vPos);
! 	    if (iRead < 11)
! 		dCharge = 0.0;
! 	    else {
! 	    	bStringToDouble( saStr[11], &dCharge );
! 		iCharges++;
! 	    }
! /* printf("--- %f [%d]\n", dCharge, iRead);*/
! /* %%% */
          }
          if ( iIndex >= iVarArrayElementCount(vaCoor) ) {
              VarArraySetSize( vaCoor, iIndex+1 );
***************
*** 1180,1185 ****
--- 1193,1211 ----
          iIndex++;
      }
  
+     if ( iCharges == 0 ) {
+         VP0(("(no charges read on atoms lines in %s)\n",
+ 						sResidueDescription(rRes) ));
+     } else {
+ 	if ( iCharges != iAtoms )
+             VP0((
+ 	      " WARNING - %d of %d atoms missing charges on atoms lines: %s\n",
+ 					iAtoms-iCharges, iAtoms,
+ 					sResidueDescription(rRes) ));
+ 	iChgWarn = 1;
+ 	iCharges = 0;
+     }
+ 
  	/* Get the last line read which is the first command */
  
      strcpy( sLine, sSave );
***************
*** 1242,1251 ****
          	goto ERROR;
  	    }
          } else if ( strcmp( saStr[1], "CHARGE" )==0 ) {
! 	    if ( iCharges )
  		VP0((
! 		"Warning: per-line charges being overridden by CHARGE block\n"
! 		));  
              iCharge = 3;
              while (1) {
                  FGETS( sLine, fIn );
--- 1268,1277 ----
          	goto ERROR;
  	    }
          } else if ( strcmp( saStr[1], "CHARGE" )==0 ) {
! 	    if ( iChgWarn )
  		VP0((
! 		"Warning: per-line charges being overridden by CHARGE block in %s\n",
! 						sResidueDescription(rRes) ));
              iCharge = 3;
              while (1) {
                  FGETS( sLine, fIn );
***************
*** 1269,1274 ****
--- 1295,1306 ----
                      iCharge++;
                  }
              }
+ 	    if ( iCharge < iAtoms ) {
+ 		    VP0(( " ERROR - incomplete CHARGE block in: %s: %d/%d\n",
+ 						sResidueDescription(rRes),
+ 						iCharge, iAtoms ));
+ 		    goto ERROR;
+ 	    }
          } else if ( strcmp( saStr[1], "IMPROPER" )==0 ) {
  	    int	problem = 0;
  	    IMPROPERt	Imp;
-----------------------------------------------------------------------------