the current default in Amber is to write trajectories and restarts in
binary format (netcdf). You can convert them in cpptraj, or you can change
this behavior by changing the appropriate input variables (see ntxo and
ioutfm in the Amber manual).
On Mon, Oct 9, 2023 at 2:09 PM Meyer, Olivia (meyerok) via AMBER <
amber.ambermd.org> wrote:
> Hello!
>
> I am completing the Computing Binding Enthalpy Tutorial for a host-guest
> complex CB7-B2 (Amber Tutorial 2.1). I am on the last step of Section 2,
> where I need to change the final box edges in the *_npt2.rst7 files.
> However, these files (*_npt2.rst7) are not human readable and I do not know
> how to change this.
>
> I have followed one of the cpptraj commands from another Archive message,
> but the following solution did not work for me:
> oliviameyer.Liv:/mnt/c/Users/LivMeyer/Desktop/Sweat_sensors_MD/cb7_b2_bindingH_tutorial$
> cpptraj b2.prmtop << EOF
> > trajin b2_npt2.rst7
> > trajout b2_npt2_new.rst7 RESTART
> > EOF
>
> CPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 10/09/23 13:44:34
> | Available memory: 5.837 GB
>
> Reading 'b2.prmtop' as Amber Topology
> Radius Set: modified Bondi radii (mbondi)
> INPUT: Reading input from 'STDIN'
> [trajin b2_npt2.rst7]
> Reading 'b2_npt2.rst7' as Amber NC Restart
> Error: Number of atoms in NetCDF file (4626) does not match number
> Error: in associated topology (4530)!
> Error: Could not set up 'b2_npt2.rst7' for reading.
> Error: Could not set up input trajectory 'b2_npt2.rst7'.
> 1 errors encountered reading input.
> TIME: Total execution time: 0.0761 seconds.
> Error: Error(s) occurred during execution.
>
> If you have any suggestions, please let me know, as I need to change the
> coordinates for each simulation (individual molecules and complex) to begin
> the next Section. Also, this is the only .prmtop file that I have so I am
> not sure why the number of atoms does not match...Thanks in advance.
>
> -Olivia
>
> Olivia K. Meyer
> Graduate Student, Kumari Lab
> University of Cincinnati
> James L. Winkle College of Pharmacy
> Department of Pharmaceutical Sciences
> 231 Albert Sabin Way, Cincinnati, OH USA 45229
>
>
>
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>
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Received on Mon Oct 09 2023 - 12:00:02 PDT
