[gmx-users] ambconv: Segmentation fault

david.evans at ulsop.ac.uk david.evans at ulsop.ac.uk
Tue Jan 11 14:56:30 CET 2005


ambconv needs an old format prmtop file, i.e. from Amber prior to
version 7. You can generate these from new format files using a
utility in the amber package, but they will have an extra (7th) digit
on the
fouth line which will cause ambconv to crash.

If this information doesn't help you, I have a patched version of the
program which 'works for me', which I could test on your files.

David Evans
School of Pharmacy 
University of London

---- Message from Sichun Yang <syang at physics.ucsd.edu> at 2005-01-10
21:59:20 ------
>I'm a new user of ambconv. I have the following the error message:
>AMBER .top               : old.prmtop
>GROMACS .top             : new.top
>AMBER .rst               : nowater.rst
>GROMACS .gro             : new.gro
>PDB .pdb                 : temp.pdb
>Segmentation fault (core dumped)
>The command I used was: 
>ambconv -v -at old.prmtop -gt new.top  -rst nowater.rst  -gro
new.gro -pdb
>I've followed the email-list and patch the changes, such as
>s_atop* atop = (s_atop*) xmalloc(sizeof(s_atop));
>#anything#_filename = (char*)
>fprintf(grotop, "  %6d%6d%s%12.5f%12.0f%s", ++atom1, ++atom2, "  
>bl, bfc,".");
>Any suggestion is welcome.
>gmx-users mailing list
>gmx-users at gromacs.org
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