[gmx-users] pdb2gmx not recognizing disulfides

Russell Green russellwgreen at gmail.com
Wed Jul 4 05:10:06 CEST 2007

Hello Mark,

a) I know for sure that the structure has a given number of disulfide bonds.
I have several other Gromacs simulations where the bonds are present
initially and stay bonded; my current problem has to do with converting this
Amber trajectory to Gromacs format (which I'm doing becuase I'm most
familiar with gromacs tools right now).

b)This structure came from a pdb crystal structure orginally. It was
properly minimized, equilibrated to 300K and simulated in a box of water for
about 10ns.

c) The structure was already minimized.

d) The only usuable structure file from Amber for gromacs conversion is in
the pdb format, which is what I used. I did use a pdb frame from later in
the trajectory but I get the same results.

The structure consists of 4 chains with disulfide bonds in several places
and some between chains. When I use the -merge option, I get problems with
the chains. When I use the -ignh option, all the cysteines are protonated
(which is not what should be happening). If I use the -ss option...nothing

Sorry for the late reply,
Russell Green

On 7/2/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> > 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
> >>pdb2gmx.
> >
> > 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
> http://www.gromacs.org/pipermail/gmx-users/2007-July/028356.html
> 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.
> Mark
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