[gmx-users] pdb2gmx not recognizing disulfides

[Russell Green]

   I did try changing the bond length but it wouldn't catch all the
disulfides. I do have multiple chains but I don't believe they should be
merged. My current work around is to just leave the disulfide residues named
CYX according to the amber format and then change them to CYS2 in the .itp
files for the corresponding .top file. This way pdb2gmx doesn't protonate
the disulfide residues and the charges for CYS2 are maintained. If anyone
thinks this is not a good idea, please tell me.

Thanks,
Russell

On 7/2/07, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
> 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
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