Re: [AMBER] Change the trajectory format.

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Thu, 25 Apr 2019 07:54:18 -0400

I've never come across a formal description of the ".dtr" trajectory
format, but a brief google search shows several software packages do
support it so it must be out there somewhere. I'll have to put it on
the to-do list...

-Dan

On Thu, Apr 25, 2019 at 2:15 AM Thomas Cheatham <tec3.utah.edu> wrote:
>
>
> > is there a way to change the trajectory produced by Anton supercomputer
> > (file.dtr) to Amber trajectory (NetCDF)?
>
> I may have missed replies, but I do not think anyone replied... In 2013,
> my approach was to read the Anton trajectories and to convert to CHARMM
> DCD format (which is simple and recognized by at least CPPTRAJ which can
> convert to whatever). I did this using VMD pulling Anton data from it's
> workdir where the "trajectories" were deposited. Replace the hard path to
> your vmd instantiation and update the frame counts (beg/end).
>
> --tec3
>
> #!/bin/csh
>
> /uufs/chpc.utah.edu/sys/pkg/vmd/vmd-std/bin/vmd -dispdev text sys0.cms <<EOF
> animate read dtr workdir/run.stk beg 0 end 20000 waitfor all 0
> animate write dcd GAAC3.dcd.1 beg 1 0
> quit
> EOF
>
>
> /uufs/chpc.utah.edu/sys/pkg/vmd/vmd-std/bin/vmd -dispdev text sys0.cms <<EOF
> animate read dtr workdir/run.stk beg 20001 end 40000 waitfor all 0
> animate write dcd GAAC3.dcd.2 beg 1 0
> quit
> EOF
>
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Received on Thu Apr 25 2019 - 05:00:02 PDT
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