Re: [AMBER] Reading grid data from standard datafile

From: Daniel Roe <>
Date: Wed, 25 Jul 2018 09:25:07 -0400

Oops - just took at look at the source code and sure enough the 3D
standard data read function is empty. I think because I normally
read/write 3D data in DX/Xplor/CCP4 format this just fell off of my
radar. I've created an issue on GitHub
( and will get to this
as soon as I can.

Sorry for the oversight!


On Wed, Jul 25, 2018 at 7:55 AM, I Lőrincz <> wrote:
> Hello!
> Exposition:
> 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
> format:
> X Y Z D
> , 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 - 06:30:02 PDT
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