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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Received on Mon Jul 02 2012 - 07:00:03 PDT
