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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Received on Mon Oct 09 2023 - 11:30:02 PDT
