Unfortunately VMD is not particularly good with writing AMBER coordinates;
they mostly handle old ASCII formats that are really no longer in use.
Also unfortunate is the fact that nobody on their development team really
has the time or resources to update to the new formats (like netcdf
restarts). I'm sure they would be quite happy to have someone write a new
reader/writer for AMBER, but as long as people can load prmtop and netcdf
trajectories, there really is no incentive to do so.
On Thu, Jul 2, 2015 at 12:31 PM, Karl Debiec <ktd3.pitt.edu> wrote:
> Hi all,
>
> I'm having difficulty reading Amber text coordinate files that have been
> written by VMD.
>
> I'm using cpptraj to analyze a set of trajectories run on Anton. My
> previous pipeline for getting them into cpptraj was to use VMD to convert
> them from Anton's binary format to Amber's text coordinate format (what VMD
> calls 'crd'), and then use cpptraj to convert them to netcdf (which VMD
> cannot write to directly). VMD's output is as follows:
>
> TITLE : Created by VMD with 1231 atoms
> -6.272 6.912 -11.783 -5.600 7.013 -10.996 -6.985 7.648 -11.604
> -5.671
> 7.198 -12.581 -6.762 5.529 -11.918 -7.619 5.628 -12.567 -5.743
> 4.606
> ...
> 21.927 4.188 -8.388 20.894 5.228 -10.236 20.653 4.187 -10.673
> 20.071
> 6.244 -10.947 20.922
> 62.856 62.856 62.856
> -5.770 6.134 -11.699 -5.159 6.220 -10.862 -6.524 6.822 -11.501
> -5.220
> ...
>
> However, cpptraj does not recognize these files as Amber coordinates,
> instead trying to read them as Tinker coordinates and failing:
>
> [trajin 0000_solute.crd ]
> Reading '0000_solute.crd' as Tinker file
> Error: Number of atoms in Tinker file changes from 7399136 to 1231
> Warning: An error occurred while determining number of frames in Tinker
> file.
> Warning: Will attempt to read -1 frames.
> Tinker file 0000_solute.crd has -1 frames.
> Error: Could not set up 0000_solute.crd for reading.
> Error: Could not set up input trajectory '0000_solute.crd'
>
> Using earlier versions of cpptraj (and VMD), though I don't know exactly
> which versions, I was able to convert the coordinates in this manner, but
> in the latest development version (from the gitosis git repo), I obtain the
> above error.
>
> I've adjusted my pipeline to instead have VMD convert them to Gromacs trr,
> which cpptraj recognizes properly. This is probably better, as it should
> retain more precision than the text intermediate (I think), but I thought
> it was worth asking the list if this behavior (cpptraj may not recognize
> Amber coordinates written by VMD) is known.
>
> Thank you,
> Karl Debiec
>
>
> --
> Karl Debiec
> Graduate Student, Molecular Biophysics & Structural Biology
> University of Pittsburgh
> Chong Group, Department of Chemistry
> Gronenborn Group, Department of Structural Biology
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Brian Radak
Postdoctoral Scholar
University of Chicago
Department of Biochemistry & Molecular Biology
Gordon Center for Integrative Science, W323A
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
e-mail: radak.uchicago.edu
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Received on Thu Jul 02 2015 - 12:00:02 PDT
