[gmx-users] pdb2gmx not recognizing disulfides

[David van der Spoel]

Russell Green wrote:
> Hello,
> 
> 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?

pdb2gmx will only make the bonds if they are within 10% of the 
equilibrium length (0.2 nm).
> 
> Thanks,
> Russell Green
> 
> On 7/1/07, *Mark Abraham* <mark.abraham at anu.edu.au 
> <mailto: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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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se