[gmx-users] pdb2gmx not recognizing disulfides

Russell Green russellwgreen at gmail.com
Mon Jul 2 16:01:45 CEST 2007

Hmm...well the thing is, I just need a .tpr file (which I was getting with
pdb2gmx followed by grompp) so I can convert an amber pdb trajectory to xtc
format. The simulation is already complete, I'm just converting it, but of
course the atoms from the tpr need to match those of the trajectory. So
should I still be doing something different other than my idea to change the
residue names of the .itp files, as mentioned previously? Sorry for some of
my ignorance, I'm still new with much of this. Thanks for all the
suggestions and input!

Russell Green

On 7/2/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Russell Green wrote:
> >
> >    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.
> >
> it's still not clear what you want to do. if your CYS are at 0.2 nm
> distance pdb2gmx will make the bonds. if they are not, why would you
> want them to form? anyway, if you want to do that, please follow
> Tsjerk's advice below.
> > Thanks,
> > Russell
> >
> > On 7/2/07, *Tsjerk Wassenaar* <tsjerkw at gmail.com
> > <mailto: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.
> >
> >
> --
> 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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