[gmx-users] make_ndx problem

David van der Spoel spoel at xray.bmc.uu.se
Sat Jun 10 20:44:28 CEST 2006

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 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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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