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

From: Chetna Tyagi <cheta231.gmail.com>
Date: Thu, 3 May 2018 16:18:54 +0200

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 production.nc files as re-doing these
simulations on my desktop computer will cost me a lot.

Best wishes

AMBER mailing list

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Received on Thu May 03 2018 - 07:30:04 PDT
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