[gmx-users] pdb2gmx not recognizing disulfides

Russell Green russellwgreen at gmail.com
Sun Jul 1 19:06:05 CEST 2007


I just changed the disulfide max bond length in the specbond.dat file to
various numbers (0.4, 0.5, 1.2, 8.0, ...) and pdb2gmx only assigns some of
the disulfides in my protein but not all. If I use 0.4, it finds 22 of the
52 CYS residues to be in disulfide bonds when all 52 should be in disulfide
bonds. And, if I use higher bond lengths the number of disulfide CYS found
decreases. Where should I look next to sort out this problem?

Russell Green

On 7/1/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:

> Did you use specbond.dat correctly?
> http://wiki.gromacs.org/index.php/specbond.dat
> Mark
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