********>Bugfix 44: Author: Scott Brozell Date: 05/20/2005 Programs: LEaP Description: tleap and xleap may cause a segmentation fault when loading a prep file containing LOOP bonds between atoms of type dummy. Fix: apply the following patch to amber8/src/leap/src/leap/amber.c ------------------------------------------------------------------------------ *** amber.c 29 Apr 2002 16:48:37 -0000 7.17 --- amber.c 21 May 2005 06:51:33 -0000 *************** *** 1189,1194 **** --- 1189,1199 ---- aMain1 = aAtom; } } + else { + if ( strncmp( sName, "DUMM", 4 ) != 0 ) { + VP0(( "Entry of type DUmmy; atom %s not created\n", sName )); + } + } cPCoor->aAtom = aAtom; iIndex++; } *************** *** 1249,1260 **** aAtom2= (ATOM)cContainerFindName( (CONTAINER)rRes, ATOMid, saStr[2] ); if ( aAtom == NULL ) { ! VP0(( "** LOOP atom %s not found\n", saStr[1] )); problem++; } if ( aAtom2 == NULL ) { ! VP0(( "** LOOP atom %s not found\n", saStr[2] )); problem++; } if (bAtomBondedTo(aAtom, aAtom2)) { VP0(( "%s: LOOP: redundant bond %s--%s ignored\n", --- 1254,1269 ---- aAtom2= (ATOM)cContainerFindName( (CONTAINER)rRes, ATOMid, saStr[2] ); if ( aAtom == NULL ) { ! VP0(( "** LOOP atom %s not found - bond not formed\n", ! saStr[1] )); problem++; + continue; } if ( aAtom2 == NULL ) { ! VP0(( "** LOOP atom %s not found - bond not formed\n", ! saStr[2] )); problem++; + continue; } if (bAtomBondedTo(aAtom, aAtom2)) { VP0(( "%s: LOOP: redundant bond %s--%s ignored\n", ------------------------------------------------------------------------------ Workarounds: Verify the LOOP bonds. Correct the dummy types of the non-dummy atoms; this may be accomplished in several ways. One way is by using a file format other than the prep file format. For example, the mol2 file format is apt for a single residue. antechamber can convert between formats, e.g.: antechamber -i input_file -fi prepi -o output_file -fo mol2