Thanks! I already made a workaround, but I'll definitely check it out.
On Fri, Jul 27, 2018, 18:28 Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> 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:
> https://github.com/Amber-MD/cpptraj/pull/624
>
> If you get a chance to try it I'd appreciate any feedback.
>
> -Dan
>
> On Wed, Jul 25, 2018 at 9:25 AM, Daniel Roe <daniel.r.roe.gmail.com>
> 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
> > (https://github.com/Amber-MD/cpptraj/issues/623) 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 <lorizoli.gmail.com> 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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>
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Received on Fri Aug 03 2018 - 11:00:02 PDT
