[gmx-users] make_ndx problem

bharat v. adkar bharat at sscu.iisc.ernet.in
Sat Jun 10 10:24:52 CEST 2006

Dear GMX users...

i have a protein-peptide complex wherein peptide does not have one of the 
terminal carboxy oxygen atoms (i.e., it has -CO only). I designate A to 
peptide and B to protein chain. when i do pdb2gmx, it adds the missing O, 
so now the group is -COO. Now with this gro file, i tried to make some 
groups with make_ndx.
when i select group 0 (system) or 1 (protein), and try to generate index 
file, i get the following error...

*** glibc detected *** double free or corruption: 0x081b5bc0 ***

but when i use any other groups to make some index file, i do not get any 
Moreover, when i solvate the system, and use the resultant gro in 
make_ndx, i get no errors with any combination of groups!!!

i am really confused.... please help...


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