[gmx-users] bug in pdb2gmx 3.3

David van der Spoel spoel at xray.bmc.uu.se
Tue Apr 18 15:07:09 CEST 2006

Hi all,

a bug was discovered and fixed in pdb2gmx from gromacs 3.3. For more 
info see http://bugzilla.gromacs.org/show_bug.cgi?id=65

This only affects proteins with a HEME group or other special bonds (may 
include disulphides as well). Please check your topology. A fix is 
available from the bugzilla website (see above). Drop the specbond.c 
file in src/kernel and recompile. Topologies generated using gromacs 
3.2.1 are fine.

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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