Re: [AMBER] writing trr trajectory

From: newamber list <>
Date: Wed, 1 Oct 2014 00:16:50 +0100


Just to add in specific I need to do some functionality available in
gromacs (g_anaeig) to "calculate the two extreme projections along a
trajectory on the average structure " which provides two extremes as pdb.

If it is possible with cpptraj then I dont need to convert in trr (but will
be worth knowing whats the issue)


On Tue, Sep 30, 2014 at 11:50 PM, newamber list <>

> Dear All
> I am converting my amber traj netcdf to gromacs trr file with cpptraj.
> When I use trr for some analysis in gromacs I get error (in gromacs) that
> atoms does not match which I have checked is not an issue.
> I suspect this might be due to absence of velocity info in my amber traj
> netcdf and trr should have velocity and force information. How cpptraj
> considers this while writing trr? I mean does it keep the original format
> of trr even if velocity info is missing in netcdf file. May be this is
> reason why gromacs can not find enough points in trr file. But again the
> trr file written by amber is read fine with vmd.
> thanks
> Jio
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Received on Tue Sep 30 2014 - 16:30:02 PDT
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