Re: [AMBER] input files from AmberTools 16/17 run on Amber14 pmemd.cuda engine problem

From: Daniel Roe <>
Date: Thu, 3 May 2018 10:32:30 -0400

The image you attached looks like you may have a mismatch between your
topology and trajectory file. Make sure you're using the same topology
that was used to generate the trajectory. Also, if your ASCII
trajectory has box coordinates make sure you select "Amber coordinates
with periodic box" - VMD will not detect this automatically.


On Thu, May 3, 2018 at 10:18 AM, Chetna Tyagi <> wrote:
> Dear all,
> I prepared prmtop and inpcrd files using Ambertools16 or 18 and ran the
> initial minimization, equilibration using sander but for the production run
> I used the university's pmemd.cuda engine of Amber14. The university server
> has only Amber14 version.
> When I try to load the resultant netcdf files .nc in VMD it shows "Could
> not open file" error and when I change it to .mdcrd format, it loads and
> looks something like this.
> The calculation runs without error reports and using the same input files
> and parameters on my AmberTools sander.MPI, no such errors occur.
> Please advice if I can correct these files as re-doing these
> simulations on my desktop computer will cost me a lot.
> --
> Best wishes
> Chetna
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
AMBER mailing list
Received on Thu May 03 2018 - 08:00:03 PDT
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