Re: [AMBER] unreadable crd files

From: Adrian Roitberg <>
Date: Thu, 4 Aug 2016 18:31:29 -0400

Amber 16 now has netcdf as a default for restart files. VMD is not able
to read them at this time.

You can try setting ntxo=1 in your mdin file or use cpptraj to read the
restart file and use trajout to write it as ascii.


On 8/4/16 5:47 PM, macc_200 wrote:
> I am using amber 16 on Ubuntu 14.04 LTS and attempting to follow the antechamber tutorial 4b.
> .
> When I try to look at the crd file from the minimization step ( using VMD (using the 1FKO_sus.prmtop file), it is unable to read the crd file. The error given is:
> Using plugin crd for coordinates from file ...........Problem reading CRD file
> When I try to create a pdb from the minimized structure using the command ambpdb -p 1FKO_sus.prmtop ....... in the tutorial, it fails with the error
> Error: Could not read restart atoms/time.
> I was able to generate a pdb file within tleap using savepdb complex 1FKO_sus.pdb and this pdb read into VMD OK but it goes wrong after that. The jobs took a sensible amount of time to run and the relevant files are there.
> Any idea what could be wrong?
> thanks,Andy.
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> AMBER mailing list

Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
AMBER mailing list
Received on Thu Aug 04 2016 - 16:00:02 PDT
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