yes, the correct way is to use the ptraj center and image commands. look in
the archives for many examples, and if you still cant' get it to work, send
your ptraj script. do check the archives first, though...
On Fri, Jun 29, 2012 at 10:42 AM, 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 Fri Jun 29 2012 - 08:00:04 PDT
