[gmx-users] pdb2gmx not recognizing disulfides
russellwgreen at gmail.com
Wed Jul 4 05:10:06 CEST 2007
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
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,
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
> > 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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