Re: [AMBER] Reading grid data from standard datafile

From: Daniel Roe <>
Date: Fri, 27 Jul 2018 12:27:49 -0400


The GitHub version of cpptraj can now read "standard" format 3D data
sets. In addition, I've thrown in a few fixes and enhancements to 3D
data handling: see here for a summary:

If you get a chance to try it I'd appreciate any feedback.


On Wed, Jul 25, 2018 at 9:25 AM, Daniel Roe <> wrote:
> 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!
> -Dan
> 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
>> _______________________________________________
>> AMBER mailing list

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Received on Fri Jul 27 2018 - 09:30:02 PDT
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