[gmx-users] pdb2gmx not recognizing disulfides

Mark Abraham mark.abraham at anu.edu.au
Tue Jul 3 03:49:09 CEST 2007

> Thanks for the tip. I didn't think to try it. But if I plan to do any
> electrostatics I still need the tpr file right? So I would need to produce
> a
> top file. Mark, you mentioned making the S-S bonds by hand.

You can see that trjconv doesn't really need a .tpr because trjconv -h
shows you that -s allows any structure file type as input. This is a
general GROMACS phenomenon.

>>You still won't get them bonded with this procedure... you need a .top
>>file with S-S bonds, and you get that by producing one by hand or using
> Could you or anyone else point me in the right direction to do this?

I'm a bit hamstrung because I don't know
a) why you are trying to make S-S bonds from a structure that has sulfurs
more than 2A apart
b) where this structure came from
c) whether you have tried the second procedure I suggested in the email
you quote http://www.gromacs.org/pipermail/gmx-users/2007-July/028337.html
d) whether you have tried the other suggestion I made

Making the topology by hand requires you to read chapter five of the
manual thoroughly and then go through a working topology with the manual
at hand so  that you understand all the bits. Only then could you hope to
make a S-S topology by hand, and then you'll probably run into hassles
with things breaking when you try to minimize with it. Much easier will be
c) or d) above.


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