[AMBER] Reading grid data from standard datafile

From: I Lőrincz <lorizoli.gmail.com>
Date: Wed, 25 Jul 2018 13:55:09 +0200


I want to calculate the time averaged charge distribution in space of a
certain part of a molecule. I used reference atoms in the rest of the
molecule to remove translation/rotation and did the rms fit. I used volmap
to calculate the density distribution of each atom in the interesting part
and wrote the distributions out to standard data files with the following
, where X,Y,Z are grid indexes and D is the prob density.
I multiplied each distrbution with the corresponding atoms partial charge
and summed them up, wrote them out to a Standard datafile of the same
format (expecting to get the charge distribution from this process). Now I
want to have a look at this. In order to do so I would need to read it back
to ptraj and use grid with the pdb option to generate a pseudo-pdb file.

Question starts here:
I can't get ptraj to read or use a Standard datafile as a grid dataset. Is
it possible? How do you create/define a grid dataset in ptraj?

Thank for any help or wise words of wisdom,
István Lőrincz
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Received on Wed Jul 25 2018 - 05:00:03 PDT
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