********>Bugfix.41:
Author: Dave Case (reported by David Mobley)
Date: 03/18/2005

Programs: tleap

Description: When a "set  pertType " command is given in tleap,
             the code should also update the PERTURBED flag for that atom
             (based on whether or not the Type and pertType strings are the
             same).  Because of an incorrect test for gibbs compatibility,
             this is not being done.  (The corresponding code for the table
             editor in xleap is correct.)

Fix:  apply the following patch to amber8/src/leap/src/leap/atom.c

------------------------------------------------------------------------------
*** atom.c	2004/03/05 22:19:04	7.20
--- atom.c	2005/03/18 19:33:06
***************
*** 1029,1035 ****
              AtomSetPertType( aAtom, "" );
          } else if ( !bObjektWarnType( oAttr, OSTRINGid ) ) return;
          AtomSetPertType( aAtom, sOString(oAttr) );
!         if( GDefaults.iGibbs ){
                  if( strcmp( sAtomType( aAtom ), sAtomPertType( aAtom ))){
                          AtomSetFlags( aAtom, ATOMPERTURB );
                  } else {
--- 1029,1035 ----
              AtomSetPertType( aAtom, "" );
          } else if ( !bObjektWarnType( oAttr, OSTRINGid ) ) return;
          AtomSetPertType( aAtom, sOString(oAttr) );
!         if( !GDefaults.iGibbs ){
                  if( strcmp( sAtomType( aAtom ), sAtomPertType( aAtom ))){
                          AtomSetFlags( aAtom, ATOMPERTURB );
                  } else {
  
------------------------------------------------------------------------------

Workarounds: You can set the PERTURBED flag with an undocumented tleap
command, but it is almost certainly better to apply this patch.