[gmx-users] Re: Problem on processing proteins consisting of two chains

[T.A.Wassenaar at chem.rug.nl]

Hi!

I would think that the effect you see is due to the periodic boundaries.
One of your subunits (which is seperate as it is not bonded to the other)
went over the boundary of the box and got in on the other side again. So
basically it is still there, but you just see the neighbouring image.
trjconv -nojump should work to get it back where it belongs (try trjconv
-h).

Hope it helps. Greetings,

Tsjerk


On Wed, 26 Nov 2003, Spiwok Vojtech wrote:

> > Dear all,
> >   I am a new user of Gromacs.I am trying to do a simulation on a protein
> > which consists of two chains(A and B) like HIV PR.Unfortunately, the two
> > chains got far away from each other. I found that two itp
> > files(protein_A.itp and protein_B.itp) were generated after using pdb2gmx.
> > It seems that Gromacs recognizes the two chains as different proteins,but
> > they belong to the same molecule indeed.
>
> Was the minimization or dynamics done in a solvent ?
> If not, this could be also result of unfavourable contact between
> atoms of each monomer that could result to spliting of dimer. I would
> either solvate the dimer before the minimization or do some
> re/constrained minimization or dynamics first.
>
> >   How can I resolve the problem? Your experiences on Gromacs will helful
> > for me.
> >
>
> Vojtech Spiwok
> ICT Prague
>
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