Oddly enough, I actually did write a batch script to process the 'pmemd' NPT simulations. However, I just noticed that I used the 'b2_npt.rst7' file for the both the b2 and cb7 systems' -restart files by accident... and overwrote the files with each new simulation... Ugh. Thank you so so much for your help. I never would've caught this. Hope you have a great rest of your day!
-Olivia
________________________________
From: Dr. Anselm Horn via AMBER <amber.ambermd.org>
Sent: Tuesday, October 10, 2023 5:05 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] .rst7 files unreadable
External Email: Use Caution
Olivia,
the general approach to reformat the coordinate file from binary to
ascii should be ok, and the commands should work in that way.
Since cpptraj complains about an inconsistency of the number of atoms in
the topology and coordinate file for your b2 system, one of your files
seems to be wrong:
The topology is reported to have 4530 atoms, while the rst7 file
contains 4626 atoms.
When looking at the sample ascii output files on the tutorial page, b2
has 4530 atoms (b2_npt2.rst7), while cb7 (cb7_npt2.rst7) has 4626.
So probably, just the file names were mixed up in the previous
simulation step in such a way that the output files were named
incorrectly: your b2_npt2.rst7 file actually is the cb7_npt2.rst7 file.
(I'd recommend to write the pmemd.cuda invocations in a batch script
file and then execute this script to prevent such an error.)
Hope that helps.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 09.10.2023 um 20:08 schrieb Meyer, Olivia (meyerok) via AMBER:
> 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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C01%7Cmeyerok%40mail.uc.edu%7Ca60d674e72f14ab5261108dbc9702736%7Cf5222e6c5fc648eb8f0373db18203b63%7C0%7C0%7C638325255755669030%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=mo%2Fjcdo%2FmF%2FMZBVSBa4bWonpEwBWjvI9HZ6IXmD4nCE%3D&reserved=0<http://lists.ambermd.org/mailman/listinfo/amber>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C01%7Cmeyerok%40mail.uc.edu%7Ca60d674e72f14ab5261108dbc9702736%7Cf5222e6c5fc648eb8f0373db18203b63%7C0%7C0%7C638325255755669030%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=mo%2Fjcdo%2FmF%2FMZBVSBa4bWonpEwBWjvI9HZ6IXmD4nCE%3D&reserved=0<
http://lists.ambermd.org/mailman/listinfo/amber>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 10 2023 - 07:30:03 PDT
