[AMBER] problem reimaging after strip WAT

From: Pablo D. Dans Puiggr˛s <pdans.mmb.pcb.ub.es>
Date: Tue, 11 Nov 2014 16:24:34 +0100


I have a reimage problem with a double helix DNA trajectory (netCDF format).

I ran a long simulation with several restart files. Since the simulation
was very long, after each restart I removed the water molecules and
stored each DNA+ions trajectory with this command (using cpptraj):

trajin md12.nc 1 -1 1
strip :WAT
trajout md12_nowat.nc netcdf

Now I want to join together all the pieces doing the usual reimaging.
I've tried several commands in cpptraj like "autoimage familiar" or
things like this:

center :1-18 mass origin
image origin center familiar
center :1-36 mass origin
image origin center familiar

but unsuccessfully! At several frames during the full trajectory the two
strands are separated. Any suggestion?

Thanking you in advance,

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Received on Tue Nov 11 2014 - 07:30:02 PST
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