Hi,
Sorry for the delay in replying - I'm quite behind these days.
On Tue, Nov 8, 2022 at 8:36 AM Damiano Spadoni via AMBER
<amber.ambermd.org> wrote:
> My issue comes from the attempts of reimaging the trajectories as I thought water molecules should be included to measure how many of those get into the different pockets. The output coming from my cpptraj script seems to have the water box centred but not the protein, the protein always looks shifted from the centre of the box and there are "cavities" in the water box. My script looks like this:
>
> parm Protein.prmtop
> trajin Protein_md10ns.mdcrd 0 last 50
> unwrap :1-1640 #the protein is 1640 amino acid long
> image origin center :1-1640 familiar
> center :1-1640 mass origin
> autoimage
> trajout Reimaged_trajectories.nc netcdf
One issue here is that the 'autoimage' command will essentially wipe
out all the previous image/center/unwrap commands, so I would start
with just 'autoimage'. The seccond issue is that you have a homodimer,
which is a bit more challenging for the 'autoimage' algorithm. Try
specifying 1 or a few residues as the "anchor" point, i.e. the point
you want to see at the center of your system. Say for example the the
active site of one of the monomers is bordered by residue 535. Try
something like:
parm Protein.prmtop
trajin Protein_md10ns.mdcrd
autoimage origin anchor :535
trajout Reimaged.nc
See if that improves things. Hope this helps,
-Dan
>
> Kind regards,
> Damiano
>
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Received on Wed Dec 07 2022 - 08:00:02 PST
