[AMBER] Imaging & centering

From: Angela de Manzanos <angela.de-manzanos11.imperial.ac.uk>
Date: Tue, 02 Jun 2015 17:33:58 +0100

Dear amber mail list users,

I am simulating a very large multimeric system and I am trying to image
it in order to study the waters that are in the active sites during the
simulation. The only way I have successfully managed to obtain a
reasonable solution using cpptraj V15.01b is by centering first all the
atoms but the solvent and ions, then imaging the solvent and ions and
finally do a second centering again of all the atoms relative to the
center of mass. The commands that I use are as follows:

trajin mysimulation.mdcrd

center !(:WAT,Na+)

image :WAT,Na+ familiar

center mass

trajout autoimage_test.nc netcdf

I know have a question about the imaging step. Am I with this set of
commands forcing the waters and Na+ in a location different from where
they are during the simulation? And if not, will this really tell me how
many waters are close to my ligand during the simulation or I am just
forcing the waters to be in the periodic box?

I am unsure about how the imaging command works and I am struggling to
find information about it, so any help on this matter would be very much


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Received on Tue Jun 02 2015 - 10:00:02 PDT
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