[gmx-users] pdb2gmx not recognizing disulfides

[Tsjerk Wassenaar]

Hi Russel,

You never mentioned the distance between the
'sulphurs-that-wouldn't-connect'. Are they beyond the range normal for
disulphide bonds? If so, you could try to add an additional entry in
the specbond.dat file with a different bond length. Maybe you'll have
to change the residue name first, although it could work without (I
don't know whether pdb2gmx properly handles multiple multiple
distances for the same atom pair, but it's easy to find out).
Another thing you never mentioned is whether the cysteines are from
one chain or from different chains. In the latter case, you have to
use the option -merge with pdb2gmx. pdb2gmx will not usually make
bonds between different chains.

Hope this helps,

Tsjerk

On 7/1/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 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
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623