I trying to build another molecule in Geant4 using your application "pdb4dna". In the case of my .pdb file, total number of atoms in each residue (nbAtom) is 52! "pdb4dna" successfully reading .pdb file when nbAtom<49. But, it does not read .pdb file when nbAtom more than 49. Error on display: *** Error in `./pdb4dna': malloc(): memory corruption: 0 En example of my .pdb file: ATOM 1 N POPCA 1 -85.938 -67.912 20.706 ATOM 2 C11 POPCA 1 -85.233 -66.984 21.693 ATOM 3 C12 POPCA 1 -86.672 -67.098 19.681 .................... ATOM 48 C312 POPCA 1 -85.321 -63.221 7.272 ATOM 49 C313 POPCA 1 -84.516 -62.900 6.005 ATOM 50 C314 POPCA 1 -85.163 -63.436 4.724 ATOM 51 C315 POPCA 1 -84.323 -63.139 3.477 ATOM 52 C316 POPCA 1 -84.941 -63.684 2.189 Please advice me, how to solve this problem and/or where is use the "free(a);" in PDBlib.cc? Best regards, B.Duurenbuyan.
*** Problem 1954 has been marked as a duplicate of this problem. ***
Hello, - does the pdb4dna example work on your system with the provided 1ZBB.pdb file ? - are you using the last version of Geant4 ? Thanks SI
Hello, - 1ZBB.pdb works fine on my machine. - Sure, I am using last version of Geant4 - I’m trying to build popc128.pdb (lipid with water molecules) in pdb4dna example. Then Geant4 makes error on display. *** Error in ‘./pdb4dna’:malloc(): memory corruption: 0 - Pdb file source: http://people.ucalgary.ca/~tieleman/download.html Thanks Duurenbuyan.B
The file you indicate is not directly from the PDB databank. If you want pdb4dna to be tested & adapted for such files, you may contact the person in charge at http://pdb4dna.in2p3.fr Thank you.
