bharat v. adkar wrote:
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 ***
Aborted
if this is reproducible then please file a bugzilla.
but when i use any other groups to make some index file, i do not get
any error....
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...
bharat
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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