[AMBER] Removing periodicity from the restart file

From: James Starlight <jmsstarlight.gmail.com>
Date: Wed, 24 Sep 2014 16:38:07 +0200

Dear Amber users!

I wounder to ask whether it possible to remove periodicity and center the
protein within the box having only restart file (no trajectory) with the
lattest coordinates as the input

typically I do it using the following tleap script:

trajin md.nc 1 last 5
reference protein.inpcrd
center :1-289 mass origin
image origin center
rms reference :1-361.CA out rmsd.dat
trajout md_proc.nc netcdf nobox

is it possible to do the same task using only .inpcrd file as the input and
to obtain output as the pdb in any pptraj one-script method?

Thanks for help,

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Received on Wed Sep 24 2014 - 08:00:02 PDT
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