On Wed, May 30, 2012, Massimiliano Porrini wrote:
>
> After having "hacked" the topology file of my system,
> so that to have the protein (which is actually a dimer) and the ligand
> belonging to the same solute molecule,
> I still see them breaking up (both the two monomers and the ligand)
> when the complex (i.e. solute) reaches the borders of the simulation box.
>
> I have also post-processed the trajectory centering and imaging the
> system (the solute has 95 residues) with the following commands:
>
>
> trajin complex_dyn.mdcrd
>
> center :1-95 mass origin
> image origin center familiar
You probably need to add the "bymask" keyword. See the example for the image
command in the ptraj section of the AmberTools manual.
....dac
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Received on Wed May 30 2012 - 08:00:02 PDT
