parmed.py and xparmed.py provide a mechanism of doing this
(combineMolecules) to make sure you don't inadvertently mess up your
topology file in the process. The topology file is a fragile beast...
All the best,
Jason
On Mon, Jul 2, 2012 at 9:40 AM, Fredrick Devadoss <
Fredrick.Devadoss.uni-konstanz.de> wrote:
> Dear Harald,
>
> I came across a similar problem, when I was running a MD simulation of a
> protein-DNA complex. DNA was out of the protein binding pocket, (as you
> said in your case the ligand), and it was somewhere in the edge of the box.
> RMSD value was also high.
>
> I think, this is because, both the molecules are treated as two different
> molecules (not a single complex). I modified the topology file, just by
> adding the number of atoms of the protein and DNA molecules, (in your case,
> number of atoms of protein and ligand molecules), and rearrange the
> topology file according to that, and run the MD simulation. It worked well
> in my case.
>
> Hope the same will work for you too.
>
> Warm regards
> Fredrick.
>
>
>
> On Friday, June 29, 2012 16:42 CEST, Harald Lanig <
> harald.lanig.chemie.uni-erlangen.de> wrote:
>
> > Dear Amber users,
> >
> > upon analysing a PBC simulation with a ligand non-covalently interacting
> > with a protein, I observed large jumps of tenth of angstroms when
> > plotting the distances between the center of masses of the protein and
> > the ligand. I attributed this to jumps caused by periodic boundary
> > conditions, placing e.g. the ligand in a different imaginary box than
> > the protein. Extracting one snap out of the trajectory clearly shows
> > that the ligand is located side-by-side to the protein, separated by
> > more than 40 angstrom.
> > Trying to image the ligand back into the box with the protein (using
> > ptraj by centering to the protein and imaging only the ligand) resulted
> > in a complex where the ligand clashes into the protein structure.
> > My question is:
> > Is this the correct way to re-generate a "normal" protein-ligand complex
> > within the same box e.g. to visualize the interactions? Is there
> > something wrong with my considerations or can you recommend me a
> > procedure to make "real" complexes for visualisation.
> >
> > Thanks a lot for any advice!
> >
> > Best wishes,
> > -Harald
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jul 02 2012 - 07:00:04 PDT
