Which version of bash are you using? "declare -n" should be present in bash versions >= 4.2. A quick fix may be to download a newer version of bash and then replace the shebang at the top of each bash file in "/path/to/FE-Workflow/bin/" with "#!/path/to/new-bash/bash"
Ryan Snyder
________________________________
From: Kankana Bhattacharjee via AMBER <amber.ambermd.org>
Sent: Monday, May 27, 2024 5:49 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Regarding FE_Workflow tool :
Dear AMBER users,
I am trying to replicate the AMBER Advanced Thermodynamic Integration
tutorial,
Link: https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial39%2Findex.php&data=05%7C02%7Crs2385%40iqb.rutgers.edu%7Cb78269bfeecf47f4cd6108dc7e327c4b%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C638524002502363296%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=Zxw2RJwBklojqOcxz0p29paXbJI9xVmjjci6Lqg4Kes%3D&reserved=0<https://ambermd.org/tutorials/advanced/tutorial39/index.php>
I am in /rbfe/ folder where input file is present and results, CDK2. I have
loaded necessary modules to activate FE_workflow, but after typing
"setup_fe", I am getting the following error:
*/apps/scratch/compile/amber22-gpu/amber22_src/FE-Workflow/bin/function-read_input.sh:
line 15: declare: -n: invalid optiondeclare: usage: declare [-aAfFgilrtux]
[-p] [name[=value]
...]/apps/scratch/compile/amber22-gpu/amber22_src/FE-Workflow/bin/function-read_input.sh:
line 15: declare: -n: invalid optiondeclare: usage: declare [-aAfFgilrtux]
[-p] [name[=value]
...]/apps/scratch/compile/amber22-gpu/amber22_src/FE-Workflow/bin/function-read_input.sh:
line 15: declare: -n: invalid optiondeclare: usage: declare [-aAfFgilrtux]
[-p] [name[=value] ...] Auto generated lambda schedule...Traceback (most
recent call last): File "gen_lambda.py", line 6, in <module> nlam =
sys.argv[1]; nlam = int (nlam)IndexError: list index out of range*
* The following lambda schedule will be usedScript currently supports only
"unified" protocol*
I am unable to figure it out.
Your suggestiosn would be highly appreciated.
Thanks & Regards
Kankana Bhattacharjee
Ph.D. Scholar
Department of Chemistry
Ashoka University
Sonipat, Haryana
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Received on Mon May 27 2024 - 07:30:02 PDT
