[gmx-users] ambconv: Segmentation fault

[david.evans at ulsop.ac.uk]

Hi,

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 ------
>
>Hi-
>
>I'm a new user of ambconv. I have the following the error message:
>AMBCONV v1.0
>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
>temp.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*)
malloc(strlen(argv[i+1])*sizeof(char)+1);
>fprintf(grotop, "  %6d%6d%s%12.5f%12.0f%s", ++atom1, ++atom2, "  
1", 
>bl, bfc,".");
>
>Any suggestion is welcome.
>
>Thanks,
>-Sichun
>
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